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X-ray structure of Mycobacterium tuberculosis cyp125 bound to the reverse type I inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X5L PDB ENTRY 2X5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 277 2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS, PH 5.5, 0.5 M NACL, 4 DEG. CELSIUS
Crystal Properties Matthews coefficient Solvent content 1.92 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.356 α = 90 b = 76.399 β = 90 c = 90.407 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 110 CCD MARRESEARCH MIRRORS 2010-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.5 50 91.9 0.04 26 7.1 56093 1.5 14.1
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 1.5 1.58 63 0.14 7.5 4.3
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 PDB ENTRY 2X5L 1.5 46.58 53185 2840 91.86 0.12487 0.12209 0.1199 0.17701 0.176 RANDOM 16.009
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] -0.24 0.21 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.742 r_dihedral_angle_4_deg 13.827 r_dihedral_angle_3_deg 12.13 r_scangle_it 6.848 r_dihedral_angle_1_deg 5.88 r_scbond_it 4.966 r_mcangle_it 3.32 r_rigid_bond_restr 2.643 r_mcbond_it 2.28 r_angle_refined_deg 1.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.742 r_dihedral_angle_4_deg 13.827 r_dihedral_angle_3_deg 12.13 r_scangle_it 6.848 r_dihedral_angle_1_deg 5.88 r_scbond_it 4.966 r_mcangle_it 3.32 r_rigid_bond_restr 2.643 r_mcbond_it 2.28 r_angle_refined_deg 1.926 r_angle_other_deg 1.387 r_chiral_restr 0.138 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_gen_planes_other 0.012 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_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3193 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing