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Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125 in complex with androstenedione
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 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.826 α = 90 b = 85.741 β = 90 c = 89.489 γ = 90
Symmetry Space Group P 21 21 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 Bruker Platinum 135 mirrors 2008-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 50 99.02 0.089 11.4 30031 30031
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 2.1 87.5 0.323 3.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 3IVY 2 49.75 30031 30031 1604 99.02 0.16341 0.16067 0.1691 0.21477 0.2209 RANDOM 15.031
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] -0.02 0.07 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.79 r_dihedral_angle_4_deg 15.186 r_dihedral_angle_3_deg 12.745 r_dihedral_angle_1_deg 5.993 r_scangle_it 4.508 r_scbond_it 3.313 r_mcangle_it 1.963 r_angle_refined_deg 1.536 r_mcbond_it 1.495 r_angle_other_deg 1.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.79 r_dihedral_angle_4_deg 15.186 r_dihedral_angle_3_deg 12.745 r_dihedral_angle_1_deg 5.993 r_scangle_it 4.508 r_scbond_it 3.313 r_mcangle_it 1.963 r_angle_refined_deg 1.536 r_mcbond_it 1.495 r_angle_other_deg 1.164 r_mcbond_other 0.623 r_nbd_refined 0.269 r_symmetry_vdw_other 0.25 r_nbd_other 0.214 r_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.123 r_nbtor_other 0.087 r_symmetry_vdw_refined 0.058 r_bond_refined_d 0.016 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 3126 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing