3HKP

Crystal structure determination of Catechol 1,2-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	3HGI	pdb entry 3HGI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	296	PEG 400 38%, MgCl2 0.1 M, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.42	α = 90
b = 37.39	β = 96.28
c = 74.1	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	IMAGE PLATE	MAR555 FLAT PANEL		2008-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.992	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	73.72	99.9	0.084	11.2	3.7		20872			18.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.85	1.95	100		0.458	3.8	3.7	3014

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	pdb entry 3HGI	1.85	34.4	19646	1063	99.14	0.19725	0.19403	0.25825	RANDOM	19.303

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]
0.54		0.49	0.71		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.811
r_dihedral_angle_4_deg	22.956
r_dihedral_angle_3_deg	16.391
r_dihedral_angle_1_deg	6.326
r_scangle_it	4.064
r_scbond_it	2.695
r_angle_refined_deg	1.716
r_mcangle_it	1.696
r_mcbond_it	1.081
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.811
r_dihedral_angle_4_deg	22.956
r_dihedral_angle_3_deg	16.391
r_dihedral_angle_1_deg	6.326
r_scangle_it	4.064
r_scbond_it	2.695
r_angle_refined_deg	1.716
r_mcangle_it	1.696
r_mcbond_it	1.081
r_nbtor_refined	0.313
r_symmetry_hbond_refined	0.276
r_symmetry_vdw_refined	0.251
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.19
r_chiral_restr	0.148
r_metal_ion_refined	0.082
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2002
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	53

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	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.