5SX7

Crystal structure of catalase-peroxidase KatG of B. pseudomallei at pH 8.5


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, pH 5.6 0.1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.1661.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.413α = 90
b = 114.948β = 90
c = 173.998γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9795ESRFBM30A

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
11.9595.9191.10.0997.94.8126909
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)
11.952950.484.6

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 REPLACEMENTTHROUGHOUT1MWV1.9520126909667390.980.1530.15110.1885RANDOM21.356
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]
0.050.02-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.077
r_dihedral_angle_4_deg17.281
r_dihedral_angle_3_deg13.904
r_dihedral_angle_1_deg5.932
r_angle_refined_deg2.101
r_mcangle_it2.092
r_mcbond_it1.422
r_mcbond_other1.42
r_angle_other_deg1.146
r_chiral_restr0.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.077
r_dihedral_angle_4_deg17.281
r_dihedral_angle_3_deg13.904
r_dihedral_angle_1_deg5.932
r_angle_refined_deg2.101
r_mcangle_it2.092
r_mcbond_it1.422
r_mcbond_other1.42
r_angle_other_deg1.146
r_chiral_restr0.142
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 Atoms1472
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing