5KQH

Crystal structure of the V293D variant of catalase-peroxidase from B. pseudomallei


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
3.261.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.787α = 90
b = 113.434β = 90
c = 174.677γ = 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-10.97944CLSI08ID-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
11.8247.56199.90.0710.0810.03814.24.3178897178897
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)
11.821.921000.4751.64.4

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 DIFFRACTIONTHROUGHOUT1MWV1.8247.561169937888999.790.15590.15440.1839RANDOM22.762
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]
-0.571.31-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.822
r_dihedral_angle_4_deg16.218
r_dihedral_angle_3_deg14.092
r_dihedral_angle_1_deg6.033
r_mcangle_it2.519
r_angle_refined_deg2.264
r_mcbond_it1.734
r_mcbond_other1.728
r_angle_other_deg1.195
r_chiral_restr0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.822
r_dihedral_angle_4_deg16.218
r_dihedral_angle_3_deg14.092
r_dihedral_angle_1_deg6.033
r_mcangle_it2.519
r_angle_refined_deg2.264
r_mcbond_it1.734
r_mcbond_other1.728
r_angle_other_deg1.195
r_chiral_restr0.161
r_bond_refined_d0.027
r_gen_planes_refined0.016
r_gen_planes_other0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11016
Nucleic Acid Atoms
Solvent Atoms1550
Heterogen Atoms135

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction