3CW9 | pdb_00003cw9

4-Chlorobenzoyl-CoA Ligase/Synthetase in the Thioester-forming Conformation, bound to 4-chlorophenacyl-CoA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T5D	1T5D, residues 1-402

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	14-18% PEG 1000, 75 mM Magnesium Nitrate, 100 mM MOPS, 1 mM AMP, 1 mM 4-Chlorophenacyl-CoA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.507	α = 90
b = 87.789	β = 90
c = 186.06	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2006-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.979469	SSRL	BL9-1

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	35	94.6	0.086	30.9	5.6	64355	60959			18.9

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	2.05	74.3		0.174	6.7		3442

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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, residues 1-402	2	35	64355	60959	3258	94.65	0.16798	0.16798	0.16576	0.17	0.20912	0.21	RANDOM	18.886

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]
1.36			-1.54		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.571
r_dihedral_angle_4_deg	17.111
r_dihedral_angle_3_deg	13.126
r_dihedral_angle_1_deg	5.64
r_scangle_it	2.176
r_scbond_it	1.323
r_angle_refined_deg	1.234
r_mcangle_it	0.759
r_mcbond_it	0.454
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.571
r_dihedral_angle_4_deg	17.111
r_dihedral_angle_3_deg	13.126
r_dihedral_angle_1_deg	5.64
r_scangle_it	2.176
r_scbond_it	1.323
r_angle_refined_deg	1.234
r_mcangle_it	0.759
r_mcbond_it	0.454
r_nbtor_refined	0.297
r_nbd_refined	0.183
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.145
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7604
Nucleic Acid Atoms
Solvent Atoms	800
Heterogen Atoms	180

Software

Software
Software Name	Purpose
SSRL	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.