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CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL ISOMERASE (VARIANT D11N) WITH BOUND PRFAR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y85 PDB ENTRY 2Y85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M HEPES PH7.5, 1.4M TRI-SODIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.56 52.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.27 α = 90 b = 63.27 β = 90 c = 131.22 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2006-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.33 20 99.1 0.04 0.58 8.4 61458 -3 16.9
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 1.33 1.4 95.8 0.58 3.4 7.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Y85 1.33 56.98 58387 3082 99.709 0.14 0.1379 0.148 0.1836 0.189 RANDOM 14.109
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] 0.109 0.109 -0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.422 r_dihedral_angle_4_deg 19.898 r_dihedral_angle_3_deg 11.95 r_scangle_it 7.261 r_dihedral_angle_1_deg 6.24 r_scbond_it 6.054 r_mcangle_it 5.129 r_mcbond_it 4.75 r_angle_refined_deg 2.206 r_angle_other_deg 1.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.422 r_dihedral_angle_4_deg 19.898 r_dihedral_angle_3_deg 11.95 r_scangle_it 7.261 r_dihedral_angle_1_deg 6.24 r_scbond_it 6.054 r_mcangle_it 5.129 r_mcbond_it 4.75 r_angle_refined_deg 2.206 r_angle_other_deg 1.183 r_symmetry_vdw_other 0.344 r_nbd_refined 0.242 r_nbd_other 0.236 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.195 r_nbtor_refined 0.191 r_symmetry_vdw_refined 0.187 r_chiral_restr 0.161 r_nbtor_other 0.116 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 1804 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing