Hi Tim,
Thanks a lot for pointing that out!
Here is the IDXREF-output from XDS, without input of unit cell constants.
Sabine
***** DETERMINATION OF THE RECIPROCAL LATTICE BASIS ******
NUMBER OF DIFFERENCE VECTOR CLUSTERS USED 200
MAXIMUM RADIUS OF DIFFERENCE VECTOR CLUSTERS (pixels) 3
MINIMUM DISTANCE BETWEEN DIFFRACTION SPOTS (pixel) 6.0
MINIMUM ALLOWED DISTANCE BETWEEN REC. LATTICE POINTS 0.2682E-02
OBSERVED BASIS CELL VOLUME 0.5948E+06
DIMENSION OF SPACE SPANNED BY DIFFERENCE VECTOR CLUSTERS 3
# COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH
1 0.0001394 0.0087644-0.0025818 0.0091378 109.44
2 0.0099426 0.0011533 0.0044729 0.0109632 91.21
3 0.0070894-0.0044146-0.0145563 0.0167819 59.59
CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS
VECTORS
# COORDINATES OF VECTOR CLUSTER FREQUENCY CLUSTER INDICES
1 -0.0198775-0.0023086-0.0089462 3033. -0.00 -2.00 0.00
2 0.0170296-0.0032635-0.0100896 2931. -0.00 1.00 1.00
3 -0.0028512-0.0055653-0.0190257 2769. 0.00 -1.00 1.00
4 0.0001345 0.0087600-0.0025802 2756. 1.00 -0.00 -0.00
5 -0.0099406-0.0011518-0.0044669 2748. -0.00 -1.00 -0.00
6 0.0369226-0.0009571-0.0011409 2572. -0.00 3.00 1.00
7 -0.0027157 0.0031989-0.0215974 2517. 1.00 -1.00 1.00
8 0.0102242 0.0186700-0.0006904 2503. 2.00 1.00 0.00
9 -0.0098018 0.0076072-0.0070529 2471. 1.00 -1.00 0.00
10 0.0096649-0.0163634 0.0096361 2465. -2.00 1.00 -0.00
11 -0.0171648-0.0055039 0.0126657 2460. -1.00 -1.00 -1.00
12 -0.0070927 0.0044138 0.0145582 2456. -0.00 -0.00 -1.00
13 0.0072273 0.0043496-0.0171271 2446. 1.00 0.00 1.00
14 0.0068016-0.0219329-0.0093878 2437. -2.00 -0.00 1.00
15 0.0197453-0.0064538 0.0115256 2428. -1.00 2.00 0.00
16 0.0100947 0.0099143 0.0018904 2413. 1.00 1.00 0.00
17 0.0073643 0.0131126-0.0197118 2403. 2.00 -0.00 1.00
18 0.0397690 0.0046107 0.0178903 2388. -0.00 4.00 0.00
19 0.0227406 0.0078707 0.0279747 2383. -0.00 3.00 -1.00
20 -0.0141824 0.0088224 0.0291127 2383. -0.00 -0.00 -2.00
21 0.0103597 0.0274362-0.0032718 2361. 3.00 1.00 0.00
22 -0.0269727 0.0021092 0.0056176 2346. -0.00 -2.00 -1.00
23 0.0340618-0.0065201-0.0201693 2329. 0.00 2.00 2.00
24 -0.0200231-0.0110674-0.0063643 2326. -1.00 -2.00 0.00
25 0.0125162-0.0108063 0.0286538 2325. -2.00 2.00 -1.00
26 -0.0126463 0.0020440-0.0260664 2323. 1.00 -2.00 1.00
27 0.0143145-0.0000672-0.0316916 2308. 1.00 -0.00 2.00
28 0.0168948-0.0120237-0.0075083 2306. -1.00 1.00 1.00
29 0.0066708-0.0307011-0.0068110 2284. -3.00 0.00 1.00
30 0.0002795 0.0175230-0.0051646 2283. 2.00 -0.00 0.00
31 -0.0226058 0.0008922-0.0305478 2283. 1.00 -3.00 1.00
32 0.0095181-0.0251297 0.0122100 2276. -3.00 1.00 0.00
33 -0.0029959-0.0143306-0.0164454 2250. -1.00 -1.00 1.00
34 0.0130704 0.0242365 0.0183371 2229. 2.00 2.00 -1.00
35 0.0267005-0.0196259-0.0004455 2214. -2.00 2.00 1.00
36 -0.0057125-0.0111320-0.0380540 2212. 0.00 -2.00 2.00
37 0.0127956 0.0067207 0.0235036 2195. -0.00 2.00 -1.00
38 0.0272584 0.0154143-0.0107700 2194. 2.00 2.00 1.00
39 0.0075127 0.0218694-0.0222930 2180. 3.00 0.00 1.00
40 0.0045134 0.0075431-0.0387461 2180. 2.00 -1.00 2.00
41 0.0298233 0.0034561 0.0134186 2169. -0.00 3.00 -0.00
42 0.0271311 0.0066555-0.0081839 2159. 1.00 2.00 1.00
43 -0.0242614-0.0010891 0.0272244 2138. -1.00 -1.00 -2.00
44 0.0341972 0.0022350-0.0227552 2121. 1.00 2.00 2.00
45 -0.0043753 0.0012122 0.0361620 2118. -1.00 1.00 -2.00
46 0.0244151 0.0098478-0.0298116 2112. 2.00 1.00 2.00
47 -0.0055691-0.0023701-0.0406352 2104. 1.00 -2.00 2.00
48 -0.0301120-0.0209742-0.0082509 2090. -2.00 -3.00 -0.00
49 -0.0296785 0.0052997-0.0159965 2086. 1.00 -3.00 0.00
50 -0.0268292 0.0108693 0.0030314 2076. 1.00 -2.00 -1.00
51 -0.0004199-0.0262847 0.0077376 2066. -3.00 -0.00 0.00
52 0.0132169 0.0330109 0.0157589 2061. 3.00 2.00 -1.00
53 -0.0005534-0.0350474 0.0103260 2049. -4.00 0.00 0.00
54 -0.0123845 0.0195574-0.0312418 2043. 3.00 -2.00 1.00
55 -0.0201672-0.0198288-0.0037871 2039. -2.00 -2.00 0.00
56 -0.0007071-0.0438227 0.0129006 2026. -5.00 -0.00 0.00
57 -0.0025795 0.0119525-0.0241882 2025. 2.00 -1.00 1.00
58 0.0396384-0.0041547 0.0204763 2025. -1.00 4.00 0.00
59 0.0196131-0.0152142 0.0141121 2020. -2.00 2.00 -0.00
60 -0.0241198 0.0076707 0.0246372 2014. -0.00 -1.00 -2.00
PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
59.59 91.21 109.44 90.03 90.05 90.09
# COORDINATES OF REC. BASIS VECTOR REDUCED CELL INDICES
1 0.0001394 0.0087644-0.0025818 0.00 -0.00 -1.00
2 0.0099426 0.0011533 0.0044729 0.00 1.00 0.00
3 0.0070894-0.0044146-0.0145563 1.00 -0.00 0.00
LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)
CHARACTER LATTICE OF FIT a b c alpha beta gamma
* 44 aP 0.0 59.9 91.6 110.0 90.0 90.0 90.0
* 31 aP 0.4 59.9 91.6 110.0 90.0 90.0 90.0
* 33 mP 0.9 59.9 91.6 110.0 90.0 90.0 90.0
* 34 mP 1.1 59.9 110.0 91.6 90.0 90.0 90.0
* 35 mP 1.2 91.6 59.9 110.0 90.0 90.0 90.0
* 32 oP 1.6 59.9 91.6 110.0 90.0 90.0 90.0
37 mC 249.7 227.9 59.9 91.6 90.0 90.0 74.8
36 oC 250.1 59.9 227.9 91.6 90.0 90.0 105.2
39 mC 250.3 192.7 59.9 110.0 90.0 90.0 71.9
28 mC 250.3 59.9 227.9 91.6 90.0 90.0 74.8
38 oC 250.7 59.9 192.7 110.0 90.0 90.0 108.1
------------------------------------------
Dr. Sabine Schneider
Research Group Leader
Technical University of Munich
Department of Chemistry
Chair of Biochemistry
Lichtenbergstr. 4
85748 Garching
Germany
Tel.: +49 (0) 89 289 13336
Fax: +49 (0) 89 289 13363
http://www.biochemie.ch.tum.de/index.php?id=919
On 11/17/2016 08:56 AM, Tim Gruene wrote:
Hi Sabine,
your reduced cell angles are exactly 90 degree. This seems unusual to me. Do
you specify the unit cell constants in XDS.INP, including a space group, or do
you leave the space group undefined? In the former case I am unsure if your
list of clusters may be biased, although it might contain half integers in
that case.
Best,
Tim
On Thursday, November 17, 2016 08:37:07 AM Sabine Schneider wrote:
Hello Kay,
I'd say yes, but I might miss something.
Here is the IDXREF.LP output:
Sabine
***** DETERMINATION OF THE RECIPROCAL LATTICE BASIS ******
NUMBER OF DIFFERENCE VECTOR CLUSTERS USED 200
MAXIMUM RADIUS OF DIFFERENCE VECTOR CLUSTERS (pixels) 3
MINIMUM DISTANCE BETWEEN DIFFRACTION SPOTS (pixel) 6.0
MINIMUM ALLOWED DISTANCE BETWEEN REC. LATTICE POINTS 0.2682E-02
OBSERVED BASIS CELL VOLUME 0.6021E+06
DIMENSION OF SPACE SPANNED BY DIFFERENCE VECTOR CLUSTERS 3
# COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH
1 0.0070481-0.0043879-0.0144998 0.0167084 59.85
2 0.0099022 0.0011565 0.0044633 0.0109230 91.55
3 -0.0001404-0.0087276 0.0025729 0.0091000 109.89
CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS
# COORDINATES OF VECTOR CLUSTER FREQUENCY CLUSTER INDICES
1 -0.0198775-0.0023086-0.0089462 3033. -0.00 -2.01 -0.00
2 0.0170296-0.0032635-0.0100896 2931. 1.01 1.00 0.00
3 -0.0028512-0.0055653-0.0190257 2769. 1.00 -1.00 0.00
4 0.0001345 0.0087600-0.0025802 2756. -0.00 -0.00 -1.00
5 -0.0099406-0.0011518-0.0044669 2748. -0.00 -1.00 -0.00
6 0.0369226-0.0009571-0.0011409 2572. 1.01 3.01 0.00
7 -0.0027157 0.0031989-0.0215974 2517. 1.00 -1.00 -1.00
8 0.0102242 0.0186700-0.0006904 2503. 0.00 1.00 -2.01
9 -0.0098018 0.0076072-0.0070529 2471. -0.00 -1.00 -1.00
10 0.0096649-0.0163634 0.0096361 2465. 0.00 1.00 2.01
11 -0.0171648-0.0055039 0.0126657 2460. -1.00 -1.00 1.00
12 -0.0070927 0.0044138 0.0145582 2456. -1.00 -0.00 -0.00
13 0.0072273 0.0043496-0.0171271 2446. 1.00 0.00 -1.00
14 0.0068016-0.0219329-0.0093878 2437. 1.00 0.00 2.01
15 0.0197453-0.0064538 0.0115256 2428. 0.00 2.01 1.00
16 0.0100947 0.0099143 0.0018904 2413. 0.00 1.00 -1.00
17 0.0073643 0.0131126-0.0197118 2403. 1.00 0.00 -2.01
18 0.0397690 0.0046107 0.0178903 2388. 0.00 4.01 0.00
19 0.0227406 0.0078707 0.0279747 2383. -1.00 3.01 0.00
20 -0.0141824 0.0088224 0.0291127 2383. -2.01 -0.00 -0.00
21 0.0103597 0.0274362-0.0032718 2361. 0.00 1.00 -3.01
22 -0.0269727 0.0021092 0.0056176 2346. -1.01 -2.01 -0.00
23 0.0340618-0.0065201-0.0201693 2329. 2.01 2.01 0.00
24 -0.0200231-0.0110674-0.0063643 2326. -0.00 -2.01 1.00
25 0.0125162-0.0108063 0.0286538 2325. -1.00 2.01 2.01
26 -0.0126463 0.0020440-0.0260664 2323. 1.00 -2.00 -1.00
27 0.0143145-0.0000672-0.0316916 2308. 2.01 0.00 -1.00
28 0.0168948-0.0120237-0.0075083 2306. 1.01 1.00 1.01
29 0.0066708-0.0307011-0.0068110 2284. 1.00 0.00 3.01
30 0.0002795 0.0175230-0.0051646 2283. -0.00 -0.00 -2.01
31 -0.0226058 0.0008922-0.0305478 2283. 1.00 -3.01 -1.00
32 0.0095181-0.0251297 0.0122100 2276. 0.00 1.00 3.01
33 -0.0029959-0.0143306-0.0164454 2250. 1.00 -1.00 1.00
34 0.0130704 0.0242365 0.0183371 2229. -1.00 2.01 -2.01
35 0.0267005-0.0196259-0.0004455 2214. 1.01 2.01 2.01
36 -0.0057125-0.0111320-0.0380540 2212. 2.01 -2.01 0.00
37 0.0127956 0.0067207 0.0235036 2195. -1.00 2.01 0.00
38 0.0272584 0.0154143-0.0107700 2194. 1.01 2.01 -2.01
39 0.0075127 0.0218694-0.0222930 2180. 1.00 0.00 -3.01
40 0.0045134 0.0075431-0.0387461 2180. 2.01 -1.00 -2.01
41 0.0298233 0.0034561 0.0134186 2169. 0.00 3.01 0.00
42 0.0271311 0.0066555-0.0081839 2159. 1.01 2.01 -1.00
43 -0.0242614-0.0010891 0.0272244 2138. -2.01 -1.01 1.00
44 0.0341972 0.0022350-0.0227552 2121. 2.01 2.01 -1.00
45 -0.0043753 0.0012122 0.0361620 2118. -2.01 1.00 1.00
46 0.0244151 0.0098478-0.0298116 2112. 2.01 1.01 -2.01
47 -0.0055691-0.0023701-0.0406352 2104. 2.01 -2.01 -1.00
48 -0.0301120-0.0209742-0.0082509 2090. -0.00 -3.01 2.01
49 -0.0296785 0.0052997-0.0159965 2086. -0.00 -3.01 -1.01
50 -0.0268292 0.0108693 0.0030314 2076. -1.01 -2.01 -1.01
51 -0.0004199-0.0262847 0.0077376 2066. 0.00 -0.00 3.01
52 0.0132169 0.0330109 0.0157589 2061. -1.00 2.01 -3.01
53 -0.0005534-0.0350474 0.0103260 2049. 0.00 0.00 4.02
54 -0.0123845 0.0195574-0.0312418 2043. 1.00 -2.01 -3.01
55 -0.0201672-0.0198288-0.0037871 2039. -0.00 -2.01 2.01
56 -0.0007071-0.0438227 0.0129006 2026. 0.00 -0.00 5.02
57 -0.0025795 0.0119525-0.0241882 2025. 1.00 -1.00 -2.01
58 0.0396384-0.0041547 0.0204763 2025. 0.00 4.02 1.01
59 0.0196131-0.0152142 0.0141121 2020. 0.00 2.01 2.01
60 -0.0241198 0.0076707 0.0246372 2014. -2.01 -1.01 -0.00
PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
59.85 91.55 109.89 90.00 90.00 90.00
# COORDINATES OF REC. BASIS VECTOR REDUCED CELL INDICES
1 0.0070481-0.0043879-0.0144998 1.00 0.00 0.00
2 0.0099022 0.0011565 0.0044633 0.00 1.00 0.00
3 -0.0001404-0.0087276 0.0025729 0.00 0.00 1.00
LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)
CHARACTER LATTICE OF FIT a b c alpha beta gamma
* 44 aP 0.0 59.9 91.6 110.0 90.0 90.0 90.0
* 31 aP 0.4 59.9 91.6 110.0 90.0 90.0 90.0
* 33 mP 0.9 59.9 91.6 110.0 90.0 90.0 90.0
* 34 mP 1.1 59.9 110.0 91.6 90.0 90.0 90.0
* 35 mP 1.2 91.6 59.9 110.0 90.0 90.0 90.0
* 32 oP 1.6 59.9 91.6 110.0 90.0 90.0 90.0
37 mC 249.7 227.9 59.9 91.6 90.0 90.0 74.8
36 oC 250.1 59.9 227.9 91.6 90.0 90.0 105.2
39 mC 250.3 192.7 59.9 110.0 90.0 90.0 71.9
28 mC 250.3 59.9 227.9 91.6 90.0 90.0 74.8
38 oC 250.7 59.9 192.7 110.0 90.0 90.0 108.1
29 mC 250.7 59.9 192.7 110.0 90.0 90.0 71.9
27 mC 500.2 192.8 59.9 143.1 90.1 127.5 71.9
On 11/17/2016 08:17 AM, Kay Diederichs wrote:
Hi Sabine,
my first guess would be that you are overlooking half of the reflections
meaning the cell has really twice the volume. Is the list of difference
vectors in IDXREF.LP clean in this respect?
Best,
Kay
On Wed, 16 Nov 2016 17:26:59 +0100, Sabine Schneider
<sabine.schnei...@cup.uni-muenchen.de> wrote:
Hello everybody,
I got a problem with solving and refining a structure of a small protein
of 20kDa, where we just swapped two residue at the surface by mutation
(AF vs FA).
For the FA variant we got three crystal forms, where we had no problem
whatsoever with MR and refinement
- P6522 cell 63 63 184 ~2.9A
- P21212 cell: 53 62 109 ~3A
- P212121 cell 40 43 96 ~1.8A
However with the AF-variant we only got one crystal (out of 50) that
diffracted reasonable well to ~2.4A at the synchrotron. And now the
problem starts: initially the data appear to be orthorhombic, but:
- SG18/19: cell 59 91 109 (I noticed that the b-axis is longer by 1/2b
compared to the other variant?!)
-> running phaser checking all possible alternative SGs found initally 2
mols/AUS in SG18, but since there was still space (and density!) I let
it search for another one (increased the clash tolerance)
SOLU SET RFZ=7.7 TFZ=11.8 PAK=0 LLG=141 TFZ==13.9 RFZ=3.0 TFZ=11.2 PAK=0
LLG=280 TFZ==17.1 LLG=288 TFZ==17.3 RFZ=5.9 TFZ=16.0 PAK=16 LLG=979
TFZ==15.3 LLG=1479 TFZ==17.4
- However the third molecule than clashes partly
- running refmac: R/Rfree stays in the high 40
- analysing the data with Xtriage indicates tNCS
- I also tried P212121, P21 and P1, always with the same result: space
as well as density between the proteins; placing more protein molecules
results in clashes (i.e. refinement in P1 gives R/Rfree of 38/41)
- data were processed with XDS as well as Dials/Aimless
- the protein is generally well folded, quite stable, without any loose
ends or flexible regions
- calculation of selfrotation functions in P21 and P21221 gives peak at
90dg (kappa=180dg)
Anyone an idea what could be going on or how to solve that?
Thanks a lot in advance!
Sabine
