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Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125, C2221 crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IVY PDB entry 3IVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 Crystallization was refined to two different conditions, both consisting of MgCl2 with 0.1 M HEPES (either pH 7.0 or 7.5) and 20% PEG 6000 or 25% PEG 3350, respectively., VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.5 α = 90 b = 118.9 β = 90 c = 145.9 γ = 90
Symmetry Space Group C 2 2 21
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 QUANTUM 315 Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focusing 2008-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.0000 Diamond I03
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 1.7 30 99.38 0.073 16.4 49511 49511
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 1.7 1.8 99.8 0.447 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3IVY 1.7 29.37 49511 49511 2689 99.38 0.15595 0.15595 0.15413 0.1623 0.18885 0.1947 RANDOM 14.769
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] 0.26 0.89 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.816 r_dihedral_angle_4_deg 15.673 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.627 r_scangle_it 2.961 r_scbond_it 2.109 r_angle_refined_deg 1.281 r_mcangle_it 1.258 r_angle_other_deg 0.951 r_mcbond_it 0.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.816 r_dihedral_angle_4_deg 15.673 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.627 r_scangle_it 2.961 r_scbond_it 2.109 r_angle_refined_deg 1.281 r_mcangle_it 1.258 r_angle_other_deg 0.951 r_mcbond_it 0.932 r_symmetry_hbond_refined 0.251 r_symmetry_vdw_refined 0.249 r_nbd_refined 0.233 r_symmetry_vdw_other 0.224 r_mcbond_other 0.208 r_nbd_other 0.199 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.178 r_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3183 Nucleic Acid Atoms Solvent Atoms 698 Heterogen Atoms 48
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling