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Crystal structure of Mycobacterium tuberculosis H37Rv orotate phosphoribosyltransferase in complex with 5-phospho-alpha-D-ribosyl 1-diphosphate (PRPP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HKI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.1M HEPES pH 7.5, 10% (w/v) PEG6000, 5% (v/v) MPD, 1mM PRPP
Crystal Properties Matthews coefficient Solvent content 2.23 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.201 α = 90 b = 58.629 β = 116.86 c = 57.224 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2014-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.899 ESRF ID23-1
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 2.25 51.05 99.3 0.045 19.66 4.7 15782 27.62
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 2.25 2.33 99.5 0.131 7.08 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5HKI 2.25 51.05 14982 788 99.17 0.18942 0.18686 0.2334 0.2389 RANDOM 41.418
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] 4.8 2.31 -1.92 -3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.113 r_dihedral_angle_4_deg 18.745 r_dihedral_angle_3_deg 15.467 r_long_range_B_other 7.218 r_long_range_B_refined 7.216 r_dihedral_angle_1_deg 6.814 r_scangle_other 5.332 r_mcangle_it 4.25 r_mcangle_other 4.249 r_scbond_it 3.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.113 r_dihedral_angle_4_deg 18.745 r_dihedral_angle_3_deg 15.467 r_long_range_B_other 7.218 r_long_range_B_refined 7.216 r_dihedral_angle_1_deg 6.814 r_scangle_other 5.332 r_mcangle_it 4.25 r_mcangle_other 4.249 r_scbond_it 3.476 r_scbond_other 3.457 r_mcbond_other 2.843 r_mcbond_it 2.842 r_angle_refined_deg 1.691 r_angle_other_deg 0.818 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2449 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling ARP model building PHASER phasing