5SW5

Crystal structure of native catalase-peroxidase KatG at pH7.5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29316-20% MPD, 0.1 M sodium citrate pH 7.6
Crystal Properties
Matthews coefficientSolvent content
3.1761.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.343α = 90
b = 114.851β = 90
c = 174.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM161.00801ESRFBM16

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.059699.30.117134.4119529
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.194.40.4812.23.47891

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 REPLACEMENTTHROUGHOUT1MWV2.0520119529635099.110.15050.14870.1843RANDOM27.088
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]
-0.10.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.015
r_dihedral_angle_4_deg15.383
r_dihedral_angle_3_deg13.495
r_dihedral_angle_1_deg5.918
r_mcangle_it2.535
r_angle_refined_deg2.141
r_mcbond_it1.81
r_mcbond_other1.803
r_angle_other_deg1.142
r_chiral_restr0.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.015
r_dihedral_angle_4_deg15.383
r_dihedral_angle_3_deg13.495
r_dihedral_angle_1_deg5.918
r_mcangle_it2.535
r_angle_refined_deg2.141
r_mcbond_it1.81
r_mcbond_other1.803
r_angle_other_deg1.142
r_chiral_restr0.142
r_bond_refined_d0.025
r_gen_planes_refined0.014
r_gen_planes_other0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11014
Nucleic Acid Atoms
Solvent Atoms1348
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing