2QVY | pdb_00002qvy

4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T5D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	277	14-22% pentaerythritol propoxylate 426, 50 mM BTP, 1 mM ATP, 1 mM 3,4-DCB, pH 6.5-6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.813	α = 90
b = 127.813	β = 90
c = 71.421	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	CCD	ADSC QUANTUM 210		2005-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F2	0.97930	CHESS	F2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.76	30	99.5	0.088	11.5	5.2		17323

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.76	2.83			0.525	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1T5D	2.76	30	16440	872	99.87	0.19455	0.19136	0.19	0.25651	0.25	RANDOM	57.054

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.47	0.23		0.47		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.099
r_dihedral_angle_4_deg	20.782
r_dihedral_angle_3_deg	20.472
r_dihedral_angle_1_deg	7.375
r_scangle_it	4.457
r_mcangle_it	4.028
r_scbond_it	3.003
r_mcbond_it	2.649
r_angle_refined_deg	1.692
r_symmetry_vdw_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.099
r_dihedral_angle_4_deg	20.782
r_dihedral_angle_3_deg	20.472
r_dihedral_angle_1_deg	7.375
r_scangle_it	4.457
r_mcangle_it	4.028
r_scbond_it	3.003
r_mcbond_it	2.649
r_angle_refined_deg	1.692
r_symmetry_vdw_refined	0.323
r_nbtor_refined	0.322
r_nbd_refined	0.242
r_symmetry_hbond_refined	0.226
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.114
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3716
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.