5SW4

Crystal structure of native catalase-peroxidase KatG at pH8.0


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, pH 5.6 0.1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.2161.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.778α = 90
b = 115.981β = 90
c = 174.844γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.97951ESRFBM30A

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
11.996.6599.90.08716.44.1144966
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)
11.91.940.4382.83.110604

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 REPLACEMENTTHROUGHOUT1MWV1.9201449661596699.760.14180.13850.1712RANDOM22.676
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]
-0.010.09-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.102
r_dihedral_angle_4_deg16.024
r_dihedral_angle_3_deg13.331
r_dihedral_angle_1_deg5.941
r_mcangle_it2.401
r_angle_refined_deg2.269
r_mcbond_it1.714
r_mcbond_other1.709
r_angle_other_deg1.188
r_chiral_restr0.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.102
r_dihedral_angle_4_deg16.024
r_dihedral_angle_3_deg13.331
r_dihedral_angle_1_deg5.941
r_mcangle_it2.401
r_angle_refined_deg2.269
r_mcbond_it1.714
r_mcbond_other1.709
r_angle_other_deg1.188
r_chiral_restr0.164
r_bond_refined_d0.029
r_gen_planes_refined0.016
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 Atoms1553
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing