3HGI | pdb_00003hgi

Crystal structure of Catechol 1,2-Dioxygenase from the gram-positive Rhodococcus opacus 1CP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BOY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	296	39% PEG400, 0.1 M Hepes, 0.1 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.794	α = 90
b = 38.118	β = 94.21
c = 76.065	γ = 90

Symmetry
Space Group	C 1 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	100	CCD	MAR CCD 165 mm		2005-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.949	EMBL/DESY, HAMBURG	BW7A

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	1.94	22.8	98.5	0.089	0.089	11.1	3.4		19038

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)
	1.94	2.05	95.6		0.264	0.264	2.6	2.4	2662

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	2BOY	1.94	20	18056	965	98.51	0.20259	0.1986	0.2	0.27755	0.28	RANDOM	30.67

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]
1.41		2.33	1.14		-2.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.142
r_dihedral_angle_4_deg	21.992
r_dihedral_angle_3_deg	13.408
r_dihedral_angle_1_deg	6.425
r_scangle_it	3.617
r_scbond_it	2.353
r_angle_refined_deg	1.573
r_mcangle_it	1.474
r_mcbond_it	0.874
r_chiral_restr	0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.142
r_dihedral_angle_4_deg	21.992
r_dihedral_angle_3_deg	13.408
r_dihedral_angle_1_deg	6.425
r_scangle_it	3.617
r_scbond_it	2.353
r_angle_refined_deg	1.573
r_mcangle_it	1.474
r_mcbond_it	0.874
r_chiral_restr	0.113
r_bond_refined_d	0.017
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2018
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	55

Software

Software
Software Name	Purpose
MAR345dtb	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.