5SYH

Structure of D141A variant of B. pseudomallei KatG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29316-20% PEG 4000, 20% MPD, 0.1 M sodium citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.1460.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.77α = 90
b = 113.45β = 90
c = 174.65γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.98CLSI08ID-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
11.6595.1495.20.0878.83.9228125
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)
11.651.7492.40.4031.83.831995

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 REPLACEMENTTHROUGHOUT1MWV1.65202167401138595.170.14190.14040.1706RANDOM21.871
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]
0.37-0.37-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.522
r_dihedral_angle_4_deg15.932
r_dihedral_angle_3_deg12.632
r_dihedral_angle_1_deg5.983
r_mcangle_it2.708
r_angle_refined_deg2.482
r_mcbond_it1.885
r_mcbond_other1.877
r_angle_other_deg1.392
r_chiral_restr0.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.522
r_dihedral_angle_4_deg15.932
r_dihedral_angle_3_deg12.632
r_dihedral_angle_1_deg5.983
r_mcangle_it2.708
r_angle_refined_deg2.482
r_mcbond_it1.885
r_mcbond_other1.877
r_angle_other_deg1.392
r_chiral_restr0.176
r_bond_refined_d0.03
r_gen_planes_refined0.017
r_gen_planes_other0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11008
Nucleic Acid Atoms
Solvent Atoms1582
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing