5KSK

Crystal structure 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
3.2662.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.703α = 90
b = 115.48β = 90
c = 174.966γ = 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-10.97949CLSI08ID-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
11.69115.4899.40.070.0810.0410.83.7225720225720
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)
11.691.7899.80.4841.63.7

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 REPLACEMENTTHROUGHOUT1MWV1.6948.3882144111116199.160.15340.1520.1796RANDOM25.904
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]
-1.091.84-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_4_deg15.92
r_dihedral_angle_3_deg13.439
r_dihedral_angle_1_deg6.105
r_mcangle_it2.982
r_angle_refined_deg2.396
r_mcbond_it2.152
r_mcbond_other2.15
r_angle_other_deg1.339
r_chiral_restr0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_4_deg15.92
r_dihedral_angle_3_deg13.439
r_dihedral_angle_1_deg6.105
r_mcangle_it2.982
r_angle_refined_deg2.396
r_mcbond_it2.152
r_mcbond_other2.15
r_angle_other_deg1.339
r_chiral_restr0.167
r_bond_refined_d0.03
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 Atoms11014
Nucleic Acid Atoms
Solvent Atoms1608
Heterogen Atoms134

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing