5KQQ

Crystal structure of the W153F variant of catalase-peroxidase from B. pseudomallei treated


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.1293MPD, 0.1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.362.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.922α = 90
b = 116.13β = 90
c = 175.788γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2015-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97959CLSI08ID-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
11.8796.990.50.08411.14.7153798
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)
11.871.9793.40.5661.34.7

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 REPLACEMENTTHROUGHOUT1MWV1.8796.9146110759990.160.14510.14350.1752RANDOM25.525
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]
-0.841.38-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.166
r_dihedral_angle_4_deg15.25
r_dihedral_angle_3_deg13.086
r_dihedral_angle_1_deg5.922
r_mcangle_it2.78
r_angle_refined_deg2.166
r_mcbond_it1.998
r_mcbond_other1.997
r_angle_other_deg1.157
r_chiral_restr0.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.166
r_dihedral_angle_4_deg15.25
r_dihedral_angle_3_deg13.086
r_dihedral_angle_1_deg5.922
r_mcangle_it2.78
r_angle_refined_deg2.166
r_mcbond_it1.998
r_mcbond_other1.997
r_angle_other_deg1.157
r_chiral_restr0.152
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 Atoms11008
Nucleic Acid Atoms
Solvent Atoms1414
Heterogen Atoms126

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction