5SX0

Crystal structure of an oxoferryl species of 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, pH 5.6 0.1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.261.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.359α = 90
b = 114.886β = 90
c = 174.626γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.00632ESRFID14-4

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
1295.98980.1357.63.7120518
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)
122.0799.90.50613504

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 REPLACEMENTTHROUGHOUT1MWV2201205181333198.010.16220.15860.1939RANDOM28.49
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]
0.47-0.610.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.554
r_dihedral_angle_4_deg16.336
r_dihedral_angle_3_deg12.764
r_dihedral_angle_1_deg5.963
r_mcangle_it2.683
r_angle_refined_deg2.004
r_mcbond_it1.867
r_mcbond_other1.859
r_angle_other_deg1.11
r_chiral_restr0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.554
r_dihedral_angle_4_deg16.336
r_dihedral_angle_3_deg12.764
r_dihedral_angle_1_deg5.963
r_mcangle_it2.683
r_angle_refined_deg2.004
r_mcbond_it1.867
r_mcbond_other1.859
r_angle_other_deg1.11
r_chiral_restr0.136
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_gen_planes_other0.009
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11011
Nucleic Acid Atoms
Solvent Atoms1225
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing