5KSG

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


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
3.2662.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.665α = 90
b = 115.928β = 90
c = 174.349γ = 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-10.9796CLSI08ID-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
11.6296.5361000.0620.0690.03115.14.9257891257891
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)
11.621.711000.5030.5030.5630.251.5537434

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 REPLACEMENTTHROUGHOUT1MWV1.6296.542448931287599.940.13570.13450.1591RANDOM20.971
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]
-0.40.78-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.682
r_dihedral_angle_4_deg14.415
r_dihedral_angle_3_deg12.881
r_dihedral_angle_1_deg5.878
r_mcangle_it2.683
r_angle_refined_deg2.682
r_mcbond_it1.942
r_mcbond_other1.938
r_angle_other_deg1.251
r_chiral_restr0.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.682
r_dihedral_angle_4_deg14.415
r_dihedral_angle_3_deg12.881
r_dihedral_angle_1_deg5.878
r_mcangle_it2.683
r_angle_refined_deg2.682
r_mcbond_it1.942
r_mcbond_other1.938
r_angle_other_deg1.251
r_chiral_restr0.177
r_bond_refined_d0.032
r_gen_planes_refined0.018
r_gen_planes_other0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11012
Nucleic Acid Atoms
Solvent Atoms1685
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing