3NVC | pdb_00003nvc

Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans in complex with salicylate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	277	8% PEG10000, pH 8.0, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.273	α = 90
b = 86.977	β = 90
c = 167.626	γ = 90

Symmetry
Space Group	I 2 2 2

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		2008-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8123	EMBL/DESY, HAMBURG	X13

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	2.45	83.918	99.1	0.079	0.079	11.7	3.4	20120	20120			52.1

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	2.45	2.58	99.5		0.477	0.477	1.6	2.9	2913

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	FOURIER SYNTHESIS	THROUGHOUT	2PHD	2.45	30	20084	1022	98.54	0.1972	0.1933	0.19	0.2724	0.27	RANDOM	45.3088

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]
2.48			2.7		-5.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.914
r_dihedral_angle_3_deg	17.988
r_dihedral_angle_4_deg	16.716
r_dihedral_angle_1_deg	7.283
r_scangle_it	3.761
r_scbond_it	2.424
r_angle_refined_deg	1.877
r_mcangle_it	1.631
r_mcbond_it	0.889
r_chiral_restr	0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.914
r_dihedral_angle_3_deg	17.988
r_dihedral_angle_4_deg	16.716
r_dihedral_angle_1_deg	7.283
r_scangle_it	3.761
r_scbond_it	2.424
r_angle_refined_deg	1.877
r_mcangle_it	1.631
r_mcbond_it	0.889
r_chiral_restr	0.121
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2735
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	29

Software

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

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.