[ccp4bb] Refmac and mixed DNA base pairs

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: CNS problem: patch statement in generate.inp
From: ºîº£·å houhf {- at -} IHEP {- dot -} AC {- dot -} CN
Date: 2008-02-29

Next message:
Subject: Re: Glu+Arg solutions for solubility
From: Lisa A Nagy lisanagy {- at -} UAB {- dot -} EDU
Date: 2008-02-29

Subject: Refmac and mixed DNA base pairs
From: Gabriel Birrane gbirrane {- at -} BIDMC {- dot -} HARVARD {- dot -} EDU
Date: 2008-02-29

Hi All,

I'm refining a structure of a protein DMA complex at 1.8A resolution.
The spacegroup is P21 and the DNA is pseudopalindromic. It looks like
I have electron density for mixed base pairs outside the palindromic
region, but Refmac5 complains when I try to model it.

ERROR: in chain E residue: 15
different residues have the same number

Any ideas would be helpful.

The problem part of the PDB is:

ATOM 3000 P A T E 15 19.137 15.018 12.002 0.50 31.84 P
ATOM 3001 P B C E 15 19.137 15.021 12.004 0.50 31.87 P
ATOM 3002 O1PA T E 15 20.174 16.043 12.238 0.50 31.52 O
ATOM 3003 O1PB C E 15 20.175 16.044 12.243 0.50 31.56 O
ATOM 3004 O2PA T E 15 19.358 13.931 11.025 0.50 33.29 O
ATOM 3005 O2PB C E 15 19.357 13.936 11.024 0.50 33.32 O
ATOM 3006 O5*A T E 15 17.761 15.720 11.621 0.50 30.16 O
ATOM 3007 O5*B C E 15 17.763 15.725 11.625 0.50 30.22 O
ATOM 3008 C5*A T E 15 16.582 14.958 11.732 0.50 30.15 C
ATOM 3009 C5*B C E 15 16.582 14.965 11.733 0.50 30.22 C
ATOM 3014 C4*A T E 15 15.394 15.866 11.970 0.50 30.69 C
ATOM 3015 C4*B C E 15 15.396 15.875 11.969 0.50 30.76 C
ATOM 3018 O4*A T E 15 15.250 16.122 13.390 0.50 27.29 O
ATOM 3019 O4*B C E 15 15.244 16.125 13.389 0.50 27.37 O
ATOM 3020 C1*A T E 15 15.262 17.523 13.611 0.50 27.99 C
ATOM 3021 C1*B C E 15 15.260 17.525 13.617 0.50 28.01 C
ATOM 3024 N1 A T E 15 15.739 17.737 15.000 0.50 26.01 N
ATOM 3025 N1 B C E 15 15.722 17.728 15.014 0.50 25.93 N
ATOM 3026 C2 A T E 15 14.790 17.829 15.992 0.50 24.94 C
ATOM 3027 C2 B C E 15 14.759 17.826 15.991 0.50 24.76 C
ATOM 3028 O2 A T E 15 13.594 17.770 15.778 0.50 25.54 O
ATOM 3029 O2 B C E 15 13.567 17.784 15.758 0.50 25.46 O
ATOM 3030 N3 A T E 15 15.291 18.004 17.251 0.50 24.47 N
ATOM 3031 N3 B C E 15 15.241 17.990 17.259 0.50 24.10 N
ATOM 3034 C4 A T E 15 16.622 18.080 17.603 0.50 24.90 C
ATOM 3035 C4 B C E 15 16.566 18.048 17.633 0.50 24.39 C
ATOM 3036 O4 A T E 15 16.968 18.236 18.767 0.50 27.65 O
ATOM 3037 N4 B C E 15 16.892 18.195 18.805 0.50 26.69 O
ATOM 3038 C5 A T E 15 17.564 17.967 16.516 0.50 25.50 C
ATOM 3039 C5 B C E 15 17.525 17.929 16.562 0.50 25.15 C
ATOM 3040 C5MA T E 15 19.038 18.042 16.786 0.50 27.79 C
ATOM 3048 C6 A T E 15 17.087 17.801 15.276 0.50 25.57 C
ATOM 3049 C6 B C E 15 17.066 17.774 15.313 0.50 25.53 C
ATOM 3052 C2*A T E 15 16.126 18.054 12.483 0.50 29.75 C
ATOM 3053 C2*B C E 15 16.136 18.056 12.499 0.50 29.79 C
ATOM 3058 C3*A T E 15 15.510 17.248 11.348 0.50 31.47 C
ATOM 3059 C3*B C E 15 15.520 17.261 11.356 0.50 31.55 C
ATOM 3062 O3*A T E 15 14.218 17.714 11.033 0.50 36.61 O
ATOM 3063 O3*B C E 15 14.233 17.736 11.039 0.50 36.71 O

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: CNS problem: patch statement in generate.inp
From: ºîº£·å houhf {- at -} IHEP {- dot -} AC {- dot -} CN
Date: 2008-02-29

Next message:
Subject: Re: Glu+Arg solutions for solubility
From: Lisa A Nagy lisanagy {- at -} UAB {- dot -} EDU
Date: 2008-02-29