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Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125 in complex with econazole
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
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.632 α = 90 b = 86.016 β = 90 c = 89.455 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 2.19 50 94.22 0.098 8.7 21805 21805
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.3
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 2.19 49.63 21805 21805 1179 94.77 0.16497 0.16108 0.1684 0.23745 0.2453 RANDOM 15.764
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] -0.08 0.05 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.945 r_dihedral_angle_4_deg 15.704 r_dihedral_angle_3_deg 14.456 r_dihedral_angle_1_deg 8.818 r_scangle_it 5.382 r_scbond_it 3.875 r_mcangle_it 2.195 r_angle_refined_deg 1.866 r_mcbond_it 1.62 r_angle_other_deg 1.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.945 r_dihedral_angle_4_deg 15.704 r_dihedral_angle_3_deg 14.456 r_dihedral_angle_1_deg 8.818 r_scangle_it 5.382 r_scbond_it 3.875 r_mcangle_it 2.195 r_angle_refined_deg 1.866 r_mcbond_it 1.62 r_angle_other_deg 1.237 r_mcbond_other 0.608 r_xyhbond_nbd_other 0.397 r_symmetry_hbond_refined 0.334 r_nbd_refined 0.265 r_xyhbond_nbd_refined 0.229 r_nbd_other 0.215 r_symmetry_vdw_other 0.214 r_nbtor_refined 0.185 r_symmetry_vdw_refined 0.143 r_chiral_restr 0.133 r_nbtor_other 0.092 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 329 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing