5SXW

Crystal structure of the E198A variant of catalase-peroxidase KatG of Burkholderia pseudomallei


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, 25 mM NaCl, 0.1 M sodium citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.261.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.34α = 90
b = 116.02β = 90
c = 174.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.696.651000.08411.95.9267341
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)
11.61.691000.552.85.538773

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 REPLACEMENTTHROUGHOUT1MWV1.6202539321340999.930.14430.1430.1691RANDOM20.949
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]
-0.120.050.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.086
r_dihedral_angle_4_deg15.739
r_dihedral_angle_3_deg13.185
r_dihedral_angle_1_deg5.82
r_angle_refined_deg2.738
r_mcangle_it2.711
r_mcbond_it1.925
r_mcbond_other1.92
r_angle_other_deg1.491
r_chiral_restr0.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.086
r_dihedral_angle_4_deg15.739
r_dihedral_angle_3_deg13.185
r_dihedral_angle_1_deg5.82
r_angle_refined_deg2.738
r_mcangle_it2.711
r_mcbond_it1.925
r_mcbond_other1.92
r_angle_other_deg1.491
r_chiral_restr0.186
r_bond_refined_d0.033
r_gen_planes_refined0.018
r_gen_planes_other0.012
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11011
Nucleic Acid Atoms
Solvent Atoms1866
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing