5SXS

Crystal structure of catalase-peroxidase KatG with isonicotinic acid hydrazide and AMP bound


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, 25 mM NaCl, 0.1 M sodium citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.1460.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.436α = 90
b = 114.172β = 90
c = 174.232γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-08-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97934CLSI08ID-1

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
11.88795.590.10.119.23.6145103
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)
11.8872870.7171.92.919880

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 REPLACEMENTTHROUGHOUT1MWV1.88720137960714390.10.16330.16180.1927RANDOM25.575
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]
0.15-0.540.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.779
r_dihedral_angle_4_deg16.357
r_dihedral_angle_3_deg13.396
r_dihedral_angle_1_deg6.18
r_mcangle_it2.404
r_angle_refined_deg2.036
r_mcbond_it1.556
r_mcbond_other1.555
r_angle_other_deg1.198
r_chiral_restr0.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.779
r_dihedral_angle_4_deg16.357
r_dihedral_angle_3_deg13.396
r_dihedral_angle_1_deg6.18
r_mcangle_it2.404
r_angle_refined_deg2.036
r_mcbond_it1.556
r_mcbond_other1.555
r_angle_other_deg1.198
r_chiral_restr0.129
r_bond_refined_d0.023
r_gen_planes_refined0.012
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 Atoms1360
Heterogen Atoms157

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing