are you mixing R3 with H3 ?
in the current pdb R3 has a=b=c, al=be=ga
while H3 has a=b, al=90, be=90, ga=120
this was not consistently used in the earlier pdb
examples
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 Z,X,Y
REMARK 290 3555 Y,Z,X
CRYST1 40.430 40.430 40.430 80.25 80.25 80.25 R 3 3
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z
REMARK 290 3555 Y-X,-X,Z
REMARK 290 4555 X+2/3,Y+1/3,Z+1/3
REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3
REMARK 290 6555 Y-X+2/3,-X+1/3,Z+1/3
REMARK 290 7555 X+1/3,Y+2/3,Z+2/3
REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3
REMARK 290 9555 Y-X+1/3,-X+2/3,Z+2/3
CRYST1 64.520 64.520 32.570 90.00 90.00 120.00 H 3 9
