3NKT | pdb_00003nkt

Crystal Structure of Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans Adducts with naphthoate

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
3.33	63.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.149	α = 90
b = 86.131	β = 90
c = 166.943	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		2009-01-01	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	2.35	46.7	94.7	0.115	0.115	11.2	4.6	21895	21895

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	96		0.44	0.44	2.47	4.7

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	2.35	30	21888	1109	94	0.1763	0.1733	0.1746	0.2335	0.2381	RANDOM	38.9106

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]
1.53			1.7		-3.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.443
r_dihedral_angle_4_deg	20.926
r_dihedral_angle_3_deg	16.06
r_dihedral_angle_1_deg	7.172
r_scangle_it	3.711
r_scbond_it	2.392
r_angle_refined_deg	1.722
r_mcangle_it	1.363
r_mcbond_it	0.733
r_chiral_restr	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.443
r_dihedral_angle_4_deg	20.926
r_dihedral_angle_3_deg	16.06
r_dihedral_angle_1_deg	7.172
r_scangle_it	3.711
r_scbond_it	2.392
r_angle_refined_deg	1.722
r_mcangle_it	1.363
r_mcbond_it	0.733
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2853
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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.