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Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4,4'-(3-((4-hydroxyphenyl)amino)-1H-pyrazole-4,5-diyl)diphenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N40 PDB entry 1N40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 2M Ammonium sulfate, 0.1M Sodium cacodylate-HCl, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.789 α = 90 b = 77.789 β = 90 c = 264.241 γ = 120
Symmetry Space Group P 65 2 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 CUSTOM-MADE 2012-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.917310 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 53.51 97.5 15.1 4 34683 34683 2 2
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 1.95 2.06 88.4 7.5 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1N40 1.95 38.89 2 32890 32890 1728 97.2 0.145 0.143 0.189 0.2139 RANDOM 15.62
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] 0.01 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.693 r_dihedral_angle_4_deg 15.92 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_1_deg 5.555 r_angle_refined_deg 2.11 r_angle_other_deg 1.805 r_chiral_restr 0.136 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.693 r_dihedral_angle_4_deg 15.92 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_1_deg 5.555 r_angle_refined_deg 2.11 r_angle_other_deg 1.805 r_chiral_restr 0.136 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.009 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 2984 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing