5KSF

Crystal structure of the D141A variant of the catalase-peroxidase from B. pseudomallei treated with acetate


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
3.2662.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.692α = 90
b = 115.474β = 90
c = 174.586γ = 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-10.9795CLSI08ID-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
11.7596.31399.60.0620.0690.0314.74.9203501203501
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)
11.751.8499.90.4811.65

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 REPLACEMENTTHROUGHOUT1MWV1.7548.3751931241020799.380.14920.14780.1751RANDOM27.877
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]
-1.122.08-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.16
r_dihedral_angle_4_deg15.775
r_dihedral_angle_3_deg13.257
r_dihedral_angle_1_deg6.044
r_mcangle_it3.314
r_angle_refined_deg2.438
r_mcbond_it2.425
r_mcbond_other2.418
r_angle_other_deg1.332
r_chiral_restr0.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.16
r_dihedral_angle_4_deg15.775
r_dihedral_angle_3_deg13.257
r_dihedral_angle_1_deg6.044
r_mcangle_it3.314
r_angle_refined_deg2.438
r_mcbond_it2.425
r_mcbond_other2.418
r_angle_other_deg1.332
r_chiral_restr0.176
r_bond_refined_d0.031
r_gen_planes_refined0.017
r_gen_planes_other0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11004
Nucleic Acid Atoms
Solvent Atoms1439
Heterogen Atoms142

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing