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Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4-(3-amino-4-(4-hydroxyphenyl)-1H-pyrazol-5-yl)benzene-1,3-diol
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 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.77 α = 90 b = 77.77 β = 90 c = 263.6 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 1.4 38.88 82.8 7.1 2.2 76131 76131 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 1.4 1.48 75.1 2.1 2.3 9977
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1N40 1.4 38.47 2 2 72290 72290 3792 81.17 0.15674 0.15536 0.155 0.18337 0.1836 RANDOM 16.951
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.279 r_dihedral_angle_4_deg 17.01 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.531 r_angle_refined_deg 2.603 r_angle_other_deg 1.9 r_chiral_restr 0.153 r_bond_refined_d 0.03 r_gen_planes_refined 0.015 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.279 r_dihedral_angle_4_deg 17.01 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.531 r_angle_refined_deg 2.603 r_angle_other_deg 1.9 r_chiral_restr 0.153 r_bond_refined_d 0.03 r_gen_planes_refined 0.015 r_gen_planes_other 0.009 r_bond_other_d 0.003 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_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2980 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing