3NST

Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans


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
3.2762.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.715α = 90
b = 87.046β = 90
c = 167.92γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-01-01MSINGLE 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
12.483.9698.40.1070.10712.44.2211002110040.159
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)
12.42.5399.30.5050.5051.54.23080

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 SYNTHESISTHROUGHOUT2PHD2.483.9221099108897.790.1550.15160.2192RANDOM35.3052
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]
1.391.72-3.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.942
r_dihedral_angle_4_deg18.195
r_dihedral_angle_3_deg16.799
r_dihedral_angle_1_deg7.252
r_scangle_it4.629
r_scbond_it2.985
r_angle_refined_deg1.928
r_mcangle_it1.866
r_mcbond_it1.033
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.942
r_dihedral_angle_4_deg18.195
r_dihedral_angle_3_deg16.799
r_dihedral_angle_1_deg7.252
r_scangle_it4.629
r_scbond_it2.985
r_angle_refined_deg1.928
r_mcangle_it1.866
r_mcbond_it1.033
r_chiral_restr0.133
r_bond_refined_d0.022
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2735
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms37

Software

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