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Crystal structure of diaminopimelate epimerase Mycobacterium tuberculosis DapF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BWZ PDB entry 1BWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9.5 291 1.9 M (NH4)H2PO4, 0.1 M bis-tris propane, pH 9.5, 2.5% glycerol, vapor diffusion, temperature 291K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 3.68 66.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.64 α = 90 b = 183.64 β = 90 c = 45.21 γ = 120
Symmetry Space Group P 65 2 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 ADSC QUANTUM Q315r 2008-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.59 45.22 99.7 0.086 0.086 13.2 14430 14430 64.8
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) 1 2.59 2.73 98.4 0.758 0.758 3.8 13 2020
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 (All) 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 1BWZ 2.6 45 14341 14341 722 99.97 0.226 0.226 0.224 0.2218 0.254 0.2545 RANDOM 38.103
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] -1.06 -0.53 -1.06 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.896 r_dihedral_angle_3_deg 18.3 r_dihedral_angle_4_deg 17.41 r_dihedral_angle_1_deg 5.639 r_scangle_it 1.609 r_angle_refined_deg 1.362 r_scbond_it 0.966 r_mcangle_it 0.817 r_mcbond_it 0.458 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.896 r_dihedral_angle_3_deg 18.3 r_dihedral_angle_4_deg 17.41 r_dihedral_angle_1_deg 5.639 r_scangle_it 1.609 r_angle_refined_deg 1.362 r_scbond_it 0.966 r_mcangle_it 0.817 r_mcbond_it 0.458 r_nbtor_refined 0.305 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2003 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 20
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction SCALA data scaling