3O5U

Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex with protocatechuate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S9A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9	296	ammonium sulphate, NaCl, TRIS, pH 9.0, vapor diffusion, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.31	α = 90
b = 87.31	β = 90
c = 185.921	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2008-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.979	EMBL/DESY, HAMBURG	X12

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	92.96	100	0.121	0.121	14.4	6.2	33380	33380			40.53

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.48	100		0.504	0.504	1.2	6.1	4866

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1S9A	2.35	30	33340	1689	99.99	0.1688	0.1663	0.2156	RANDOM	42.1042

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]
0.83	0.42		0.83		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.25
r_dihedral_angle_4_deg	22.189
r_dihedral_angle_3_deg	15.044
r_dihedral_angle_1_deg	9.75
r_scangle_it	4.023
r_scbond_it	2.474
r_mcangle_it	1.695
r_angle_refined_deg	1.63
r_mcbond_it	0.898
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.25
r_dihedral_angle_4_deg	22.189
r_dihedral_angle_3_deg	15.044
r_dihedral_angle_1_deg	9.75
r_scangle_it	4.023
r_scbond_it	2.474
r_mcangle_it	1.695
r_angle_refined_deg	1.63
r_mcbond_it	0.898
r_chiral_restr	0.109
r_bond_refined_d	0.017
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4062
Nucleic Acid Atoms
Solvent Atoms	337
Heterogen Atoms	122

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
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.