2CCD

Crystal structure of the catalase-peroxidase (KatG) and S315T mutant from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CC4PDB ENTRY 2CC4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.66% PEG4000, 0.1M NA ACETATE, PH4.6, 0.17MM N-DODECYL-B-D-MALTOSIDE PROTEIN CONCENTRATION OF 16MG/ML, pH 4.60
Crystal Properties
Matthews coefficientSolvent content
2.754.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.807α = 90
b = 149.807β = 90
c = 154.493γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
12.12078.50.12103.376312
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)
12.12.17640.281.91.8

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 2CC42.12076312398678.50.2320.230.276RANDOM20.27
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]
-1.5-1.52.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.854
r_dihedral_angle_4_deg17.274
r_dihedral_angle_3_deg17.057
r_dihedral_angle_1_deg5.96
r_scangle_it1.942
r_angle_refined_deg1.392
r_scbond_it1.338
r_mcangle_it0.796
r_mcbond_it0.549
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.854
r_dihedral_angle_4_deg17.274
r_dihedral_angle_3_deg17.057
r_dihedral_angle_1_deg5.96
r_scangle_it1.942
r_angle_refined_deg1.392
r_scbond_it1.338
r_mcangle_it0.796
r_mcbond_it0.549
r_nbtor_refined0.306
r_symmetry_hbond_refined0.235
r_nbd_refined0.215
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.173
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms11034
Nucleic Acid Atoms
Solvent Atoms595
Heterogen Atoms86

Software

Software
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
XTALVIEWphasing
REFMACrefinement