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The Crystal Structure of Rv2623 from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQ8 PDB ENTRY 1TQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 277 29% polyacrylate 5100, 100mM sodium citrate, 20mM MgCl2, 200mM MES, pH 5.4, vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.78 74.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.975 α = 90 b = 241.48 β = 90 c = 241.659 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 315 2006-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 50 98.1 0.088 14.4 5 121857 121857
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 95.6 0.508 0.508 2.013 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1TQ8 2.9 49.57 121857 105356 5560 99.02 0.25136 0.25047 0.249 0.26817 0.252 RANDOM 48.106
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] 4.57 -2.96 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.258 r_dihedral_angle_3_deg 15.893 r_dihedral_angle_4_deg 13.849 r_dihedral_angle_1_deg 4.585 r_mcangle_it 2.272 r_mcbond_it 1.637 r_scangle_it 1.242 r_angle_refined_deg 0.979 r_scbond_it 0.719 r_symmetry_hbond_refined 0.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.258 r_dihedral_angle_3_deg 15.893 r_dihedral_angle_4_deg 13.849 r_dihedral_angle_1_deg 4.585 r_mcangle_it 2.272 r_mcbond_it 1.637 r_scangle_it 1.242 r_angle_refined_deg 0.979 r_scbond_it 0.719 r_symmetry_hbond_refined 0.337 r_nbtor_refined 0.317 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.23 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.054 r_bond_refined_d 0.011 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17267 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 512
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction