Dear Kavya, I would examine the electron density of your Arginine. It may be present in two alternative conformations and you may have fitted the Arginine in the middle, e.g. with the NH1 in one conformation and the NH2 in the other.
The Arginine may also just be incorrectly fitted. Using Coot with "Auto Fit Rotatmer" and "Real Space Refine Zone" you might be able to correct it. Just using "Regularize Zone" on the Arginine might give hints how the Arginine got distorted. However, before running another round of refinement, it needs to be fitted back in electron density. Best, Herman -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Kavyashree Manjunath Sent: Monday, April 15, 2013 9:41 AM To: [email protected] Subject: Re: [ccp4bb] Angle restraints Sir, I used RCSB validation server. Deviations are as given below - Deviation Resi AT1 - AT2 - AT3 Bond Dict Std Angle Value Dev -------------------------------------------------------------- 3.2 ARG NE - CZ - NH1 123.5 120.3 0.5 -3.4 ARG NE - CZ - NH2 116.9 120.3 0.5 Thus its more than 6 sigmas in both the cases. Its not an outlier. zANGL is 0.628 and Rms BondAngle is 1.4077. would you suggest me to ignore this deviation? But will it not be a problem during PDB submission? What is the reason I am getting a deviation like this? Should I reduce the weighing term further down? Thanking you Regards Kavya > Hi Kavya, > > Which validation program did you use? How big is the deviation (in > sigma values)? Is it the only outlier? What is your overall bond angle rmsZ? > > Using external restraints is a bit over the top here, especially if it > is the only outlier. If your rmsZ is high (close to or over 1) then > you may want to try tighter geometric restraints overall. > In a normal distribution it is not surprising to find a 'true' > outlier, so if your structure is large you need to worry less. > > Cheers, > Robbie > > Sent from my Windows Phone > ________________________________ > From: Kavyashree Manjunath > Sent: 2013-04-15 07:13 > To: [email protected] > Subject: [ccp4bb] Angle restraints > > Dear users, > > Validation of a structure showed a deviation in the angle between > atoms NH1-CZ-NE and NH2-CZ-NE in the arginine residue. Several trials > of modification of the orientation failed to solve this problem. I > also confirmed by deleting the side chain and refining, it confirmed > the presence of complete side chain. So I proceeded to use external > restraints for these two angles in refmac5 (version 5.6.0117). > > The keyword was as follows - > external angle first chain A residue 93 atom NE next chain A residue > 93 atom CZ next chain A residue 93 atom NH1 value 120.3 sigma 0.5 > external angle first chain A residue 93 atom NH2 next chain A residue > 93 atom CZ next chain A residue 93 atom NE value 120.3 sigma 0.5 > > Still there is no change in the angle, it continues to have the same > deviation. > > So kindly suggest whether there is any error in the keyword provided > or other way to handle this problem. > > Thanking you > Regards > Kavya > > > -- > This message has been scanned for viruses and dangerous content by > MailScanner, and is believed to be clean. > > -- > This message has been scanned for viruses and dangerous content by > MailScanner, and is believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
