5SYW

Crystal structure of Burkhoderia pseudomallei KatG variant Q233E


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
3.1761.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.019α = 90
b = 114.195β = 90
c = 174.668γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-07-09MSINGLE 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
11.8595.5898.80.07511.13.6170117
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)
11.851.9599.50.5031.53.7

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 REPLACEMENTTHROUGHOUT1MWV1.8520161698841998.790.15110.14950.1821RANDOM26.058
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]
-1.282.98-1.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.581
r_dihedral_angle_4_deg13.948
r_dihedral_angle_3_deg12.953
r_dihedral_angle_1_deg5.958
r_mcangle_it2.821
r_angle_refined_deg2.151
r_mcbond_it1.998
r_mcbond_other1.993
r_angle_other_deg1.239
r_chiral_restr0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.581
r_dihedral_angle_4_deg13.948
r_dihedral_angle_3_deg12.953
r_dihedral_angle_1_deg5.958
r_mcangle_it2.821
r_angle_refined_deg2.151
r_mcbond_it1.998
r_mcbond_other1.993
r_angle_other_deg1.239
r_chiral_restr0.148
r_bond_refined_d0.025
r_gen_planes_refined0.014
r_gen_planes_other0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11014
Nucleic Acid Atoms
Solvent Atoms1458
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing