3NVC

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)
TypeSourceAccession CodeDetails
experimental modelPDB 2PHD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION82778% PEG10000, pH 8.0, vapor diffusion, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2962.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.273α = 90
b = 86.977β = 90
c = 167.626γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8123EMBL/DESY, HAMBURGX13

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4583.91899.10.0790.07911.73.4201202012052.1
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)RedundancyNumber Unique Reflections (All)
12.452.5899.50.4770.4771.62.92913

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2PHD2.453020084102298.540.19720.19330.2724RANDOM45.3088
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]
2.482.7-5.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.914
r_dihedral_angle_3_deg17.988
r_dihedral_angle_4_deg16.716
r_dihedral_angle_1_deg7.283
r_scangle_it3.761
r_scbond_it2.424
r_angle_refined_deg1.877
r_mcangle_it1.631
r_mcbond_it0.889
r_chiral_restr0.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.914
r_dihedral_angle_3_deg17.988
r_dihedral_angle_4_deg16.716
r_dihedral_angle_1_deg7.283
r_scangle_it3.761
r_scbond_it2.424
r_angle_refined_deg1.877
r_mcangle_it1.631
r_mcbond_it0.889
r_chiral_restr0.121
r_bond_refined_d0.018
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2735
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms29

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection