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Crystal structure of Mycobacterium tuberculosis CYP126A1 in complex with 1-(3-(1H-imidazol-1-yl)propyl)-3-((3s,5s,7s)-adamantan-1-yl)urea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2M sodium sulphate, 0.1 M Hepes pH 7.5 and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.25 α = 90 b = 69.91 β = 90 c = 226.14 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 PIXEL DECTRIS PILATUS 300K 2011-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 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 1.58 57.31 99.8 0.024 20.1 7.3 122489
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 1.58 1.62 100 0.829 2.6 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1OXA 1.58 57.31 122488 6486 100 0.17176 0.1701 0.1782 0.20327 0.2111 RANDOM 16.426
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] 0.11 0.24 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.535 r_dihedral_angle_4_deg 17.701 r_dihedral_angle_3_deg 13.774 r_dihedral_angle_1_deg 5.748 r_scangle_it 5.353 r_scbond_it 3.404 r_mcangle_it 2.26 r_angle_refined_deg 2.056 r_mcbond_it 1.333 r_angle_other_deg 1.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.535 r_dihedral_angle_4_deg 17.701 r_dihedral_angle_3_deg 13.774 r_dihedral_angle_1_deg 5.748 r_scangle_it 5.353 r_scbond_it 3.404 r_mcangle_it 2.26 r_angle_refined_deg 2.056 r_mcbond_it 1.333 r_angle_other_deg 1.124 r_mcbond_other 0.443 r_chiral_restr 0.139 r_bond_refined_d 0.027 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other 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 5881 Nucleic Acid Atoms Solvent Atoms 998 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling