4FAG | pdb_00004fag

Crystal Structure of the Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans W104Y mutant in complex with gentisate

X-RAY DIFFRACTION

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
3.37	63.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.351	α = 90
b = 87.908	β = 90
c = 167.078	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		2009-06-16	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	2.5	57.17	97.5	0.094	0.094	9.7	3		18973

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	2.5	2.64	98.3		0.392	0.392	2.2	3	2767

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.5	38.9	18971	968	96.69	0.1958	0.192	0.19	0.2681	0.26	RANDOM	47.4035

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]
0.2			0.09		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.1
r_dihedral_angle_4_deg	20.168
r_dihedral_angle_3_deg	19.792
r_dihedral_angle_1_deg	7.598
r_scangle_it	3.555
r_scbond_it	2.193
r_angle_refined_deg	1.918
r_mcangle_it	1.667
r_mcbond_it	0.899
r_chiral_restr	0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.1
r_dihedral_angle_4_deg	20.168
r_dihedral_angle_3_deg	19.792
r_dihedral_angle_1_deg	7.598
r_scangle_it	3.555
r_scbond_it	2.193
r_angle_refined_deg	1.918
r_mcangle_it	1.667
r_mcbond_it	0.899
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	2827
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	18

Software

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