5SYK

Crystal structure of B. pseudomallei KatG treated with hydrogen peroxide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MWV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29316-20% PEG 4000, 20% MPD, 0.1 M sodium citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.2161.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.72α = 90
b = 116.2β = 90
c = 174.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.96CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.896.7594.70.0858.63.4170004
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.995.70.4811.53

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1MWV1.820170004887894.710.14980.14830.1792RANDOM22.885
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]
0.41-0.970.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.82
r_dihedral_angle_4_deg16.346
r_dihedral_angle_3_deg13.166
r_dihedral_angle_1_deg6.18
r_mcangle_it2.655
r_angle_refined_deg2.2
r_mcbond_it1.804
r_mcbond_other1.803
r_angle_other_deg1.266
r_chiral_restr0.151
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.82
r_dihedral_angle_4_deg16.346
r_dihedral_angle_3_deg13.166
r_dihedral_angle_1_deg6.18
r_mcangle_it2.655
r_angle_refined_deg2.2
r_mcbond_it1.804
r_mcbond_other1.803
r_angle_other_deg1.266
r_chiral_restr0.151
r_bond_refined_d0.026
r_gen_planes_refined0.015
r_gen_planes_other0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11014
Nucleic Acid Atoms
Solvent Atoms1487
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing