4C50

Crystal Structure of the Catalase-Peroxidase (KatG) D137S mutant from Mycobacterium Tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CCAPDB ENTRY 2CCA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6100 MM SODIUM ACETATE, PH 4.6, 6% PEG 4000, AND 0.17 MM N-DODECYL-BETA-D-MALTOSIDE
Crystal Properties
Matthews coefficientSolvent content
2.8356.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.59α = 90
b = 150.59β = 90
c = 157.35γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.575.399.90.138.76.2629426
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)
12.52.561000.393.96.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2CCA2.575.4159676318899.750.266050.263630.31113RANDOM34.25
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]
-0.06-0.060.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg15.825
r_dihedral_angle_3_deg15.714
r_dihedral_angle_1_deg5.774
r_mcangle_it4.068
r_mcbond_it2.492
r_mcbond_other2.491
r_scbond_it2.123
r_angle_refined_deg1.426
r_angle_other_deg0.833
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg15.825
r_dihedral_angle_3_deg15.714
r_dihedral_angle_1_deg5.774
r_mcangle_it4.068
r_mcbond_it2.492
r_mcbond_other2.491
r_scbond_it2.123
r_angle_refined_deg1.426
r_angle_other_deg0.833
r_chiral_restr0.075
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11048
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing