6CDQ

Crystal structure of the W202F variant of catalase-peroxidase from B. pseudomallei with INH bound.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.1293MPD, 0.1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.2361.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.531α = 90
b = 114.896β = 90
c = 174.099γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2017-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-10.98CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.92174.09988.80.0780.0930.0489.43.3136130136130
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.922.0297.30.5160.5160.6180.3311.53.2

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 REPLACEMENTTHROUGHOUTPDBID 1MWV1.92174.099129234684588.40.16760.16590.1989RANDOM26.538
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]
-0.591.62-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.544
r_dihedral_angle_4_deg17.749
r_dihedral_angle_3_deg14.022
r_dihedral_angle_1_deg6.708
r_angle_refined_deg1.399
r_angle_other_deg0.764
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.012
r_gen_planes_other0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.544
r_dihedral_angle_4_deg17.749
r_dihedral_angle_3_deg14.022
r_dihedral_angle_1_deg6.708
r_angle_refined_deg1.399
r_angle_other_deg0.764
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.012
r_gen_planes_other0.009
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11004
Nucleic Acid Atoms
Solvent Atoms1272
Heterogen Atoms152

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing