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Crystal structure of the catalase-peroxidase (KatG) and S315T mutant from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CC4 PDB ENTRY 2CC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 6% 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 coefficient Solvent content 2.7 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.807 α = 90 b = 149.807 β = 90 c = 154.493 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2004-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 20 78.5 0.12 10 3.3 76312
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.17 64 0.28 1.9 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CC4 2.1 20 76312 3986 78.5 0.232 0.23 0.2368 0.276 0.2775 RANDOM 20.27
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 -1.5 2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.854 r_dihedral_angle_4_deg 17.274 r_dihedral_angle_3_deg 17.057 r_dihedral_angle_1_deg 5.96 r_scangle_it 1.942 r_angle_refined_deg 1.392 r_scbond_it 1.338 r_mcangle_it 0.796 r_mcbond_it 0.549 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.854 r_dihedral_angle_4_deg 17.274 r_dihedral_angle_3_deg 17.057 r_dihedral_angle_1_deg 5.96 r_scangle_it 1.942 r_angle_refined_deg 1.392 r_scbond_it 1.338 r_mcangle_it 0.796 r_mcbond_it 0.549 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 Atoms Number Protein Atoms 11034 Nucleic Acid Atoms Solvent Atoms 595 Heterogen Atoms 86
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing XTALVIEW phasing REFMAC refinement