5SW6

Crystal structure of an oxoferryl species of catalase-peroxidase KatG at pH5.6


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
3.1560.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.211α = 90
b = 114.658β = 90
c = 174.378γ = 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
11.995.898.90.09522.57.3140763
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)
11.91.9797.90.42715339

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 REPLACEMENTTHROUGHOUT1MWV1.9201407631552298.780.14450.14120.1749RANDOM21.145
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]
-0.070.31-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.027
r_dihedral_angle_4_deg18.47
r_dihedral_angle_3_deg13.096
r_dihedral_angle_1_deg5.978
r_mcangle_it2.42
r_angle_refined_deg2.183
r_mcbond_it1.617
r_mcbond_other1.613
r_angle_other_deg1.164
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.027
r_dihedral_angle_4_deg18.47
r_dihedral_angle_3_deg13.096
r_dihedral_angle_1_deg5.978
r_mcangle_it2.42
r_angle_refined_deg2.183
r_mcbond_it1.617
r_mcbond_other1.613
r_angle_other_deg1.164
r_chiral_restr0.154
r_bond_refined_d0.026
r_gen_planes_refined0.015
r_gen_planes_other0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11010
Nucleic Acid Atoms
Solvent Atoms1501
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALAdata scaling
AMoREphasing