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Structure of Mycobacterium tuberculosis Ribose-5-Phosphate Isomerase, RpiB, Rv2465c, in complex with 4-phospho-D-erythronohydroxamic acid.
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 1.55 M AMMONIUM PHOSPHATE, 0.1 M HEPES, PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.8 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.479 α = 90 b = 102.855 β = 95.37 c = 69.545 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 MIRRORS 2003-11-08 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 2.1 81.65 99.9 0.12 5.3 3.2 55757 2.5
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 2.1 2.2 99.9 0.36 2.5 3.1
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 2.1 81.65 52926 2830 99.9 0.203 0.202 0.2083 0.221 0.2289 RANDOM 19.65
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] -0.51 -1.1 -0.53 0.83
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 3.794 r_dihedral_angle_1_deg 3.786 r_angle_refined_deg 1.441 r_scangle_it 0.8 r_scbond_it 0.434 r_mcangle_it 0.385 r_symmetry_vdw_other 0.263 r_nbd_other 0.243 r_mcbond_it 0.204 r_nbd_refined 0.162
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 3.794 r_dihedral_angle_1_deg 3.786 r_angle_refined_deg 1.441 r_scangle_it 0.8 r_scbond_it 0.434 r_mcangle_it 0.385 r_symmetry_vdw_other 0.263 r_nbd_other 0.243 r_mcbond_it 0.204 r_nbd_refined 0.162 r_symmetry_vdw_refined 0.112 r_nbtor_other 0.106 r_symmetry_hbond_refined 0.098 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_gen_planes_other 0.002 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 5929 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling