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Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with the inhibitor 5-deoxy-5-phospho-D- ribonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1USL PDB ENTRY 1USL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 15% PEG 8000,0.1 M MES PH6, 5% PEG 1000, 0.2 M LISO4
Crystal Properties Matthews coefficient Solvent content 2.79 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.369 α = 90 b = 102.119 β = 96.18 c = 69.604 γ = 90
Symmetry Space Group C 1 2 1
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 2005-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 81.65 98.5 0.09 9.7 2.6 62962 3 17
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 2.11 97.7 0.39 3 2.6
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 1USL 2 50 59767 3193 98.3 0.161 0.159 0.1659 0.193 0.2011 RANDOM 12.1
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] -0.48 -0.37 -0.01 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.579 r_dihedral_angle_4_deg 19.353 r_dihedral_angle_3_deg 12.943 r_dihedral_angle_1_deg 6.334 r_scangle_it 2.27 r_mcangle_it 2.077 r_mcbond_it 1.458 r_scbond_it 1.454 r_angle_refined_deg 1.408 r_angle_other_deg 1.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.579 r_dihedral_angle_4_deg 19.353 r_dihedral_angle_3_deg 12.943 r_dihedral_angle_1_deg 6.334 r_scangle_it 2.27 r_mcangle_it 2.077 r_mcbond_it 1.458 r_scbond_it 1.454 r_angle_refined_deg 1.408 r_angle_other_deg 1.008 r_symmetry_vdw_other 0.327 r_nbd_refined 0.237 r_nbd_other 0.202 r_nbtor_refined 0.169 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.138 r_symmetry_vdw_refined 0.131 r_nbtor_other 0.085 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5915 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing