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Crystal structure of Mycobacterium tuberculosis H37Rv orotate phosphoribosyltransferase in complex with Fe(III) dicitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.01M Iron(III) chloride hexahydrate, 0.1M Sodium citrate tribasic dihydrate pH 6.1, 10% (v/v) Jeffamine M-600
Crystal Properties Matthews coefficient Solvent content 2.67 54.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.421 α = 85.64 b = 60.262 β = 89.9 c = 65.181 γ = 79.96
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 6M 2014-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 2.4 42.17 95.3 0.11 8.74 3.7 18336
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 2.4 2.49 94.4 0.43 2.78 3.7
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 2P1Z 2.4 64.99 27688 1477 95.25 0.19849 0.19514 0.2003 0.26015 0.2617 RANDOM 35.789
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] -1.53 -0.37 2.58 2.08 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.572 r_dihedral_angle_3_deg 16.036 r_dihedral_angle_4_deg 14.156 r_long_range_B_refined 6.744 r_long_range_B_other 6.607 r_dihedral_angle_1_deg 6.387 r_scangle_other 4.63 r_mcangle_it 3.832 r_mcangle_other 3.831 r_scbond_it 3.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.572 r_dihedral_angle_3_deg 16.036 r_dihedral_angle_4_deg 14.156 r_long_range_B_refined 6.744 r_long_range_B_other 6.607 r_dihedral_angle_1_deg 6.387 r_scangle_other 4.63 r_mcangle_it 3.832 r_mcangle_other 3.831 r_scbond_it 3.674 r_scbond_other 2.936 r_mcbond_it 2.469 r_mcbond_other 2.457 r_angle_refined_deg 1.843 r_angle_other_deg 1.013 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5104 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling ARP model building