5SX6

Crystal structure of the catalase-peroxidase KatG of B. pseudomallei at pH 6.5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29316-20% PEG 4000, 20% MPD, pH 5.6 0.1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.1761.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.529α = 90
b = 114.795β = 90
c = 174.647γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.995.9399.80.07510.87.4150790
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)
11.91.9599.70.387.5

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 REPLACEMENTTHROUGHOUT1MWV1.920150790788899.720.14110.13940.1724RANDOM24.992
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]
0.010.19-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.161
r_dihedral_angle_4_deg17.255
r_dihedral_angle_3_deg13.309
r_dihedral_angle_1_deg5.966
r_mcangle_it2.656
r_angle_refined_deg2.329
r_mcbond_it1.945
r_mcbond_other1.934
r_angle_other_deg1.2
r_chiral_restr0.173
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.161
r_dihedral_angle_4_deg17.255
r_dihedral_angle_3_deg13.309
r_dihedral_angle_1_deg5.966
r_mcangle_it2.656
r_angle_refined_deg2.329
r_mcbond_it1.945
r_mcbond_other1.934
r_angle_other_deg1.2
r_chiral_restr0.173
r_bond_refined_d0.029
r_gen_planes_refined0.017
r_gen_planes_other0.011
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11014
Nucleic Acid Atoms
Solvent Atoms1458
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing