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Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor LL-AziDAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2.8 M sodium acetate and 0.1 M HEPES (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.394 α = 90 b = 104.02 β = 90 c = 59.936 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 210 2005-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115869 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.35 30 95.17 63225 63225
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.4 86.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.35 30 63225 63225 3204 95.17 0.13906 0.13906 0.13753 0.16831 0.1578 RANDOM 10.417
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] -0.62 0.29 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.399 r_dihedral_angle_4_deg 11.819 r_dihedral_angle_3_deg 10.45 r_dihedral_angle_1_deg 6.62 r_sphericity_free 5.854 r_scangle_it 4.717 r_scbond_it 3.446 r_rigid_bond_restr 3.163 r_sphericity_bonded 2.786 r_mcangle_it 2.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.399 r_dihedral_angle_4_deg 11.819 r_dihedral_angle_3_deg 10.45 r_dihedral_angle_1_deg 6.62 r_sphericity_free 5.854 r_scangle_it 4.717 r_scbond_it 3.446 r_rigid_bond_restr 3.163 r_sphericity_bonded 2.786 r_mcangle_it 2.266 r_mcbond_it 1.898 r_angle_refined_deg 1.508 r_angle_other_deg 0.714 r_mcbond_other 0.708 r_symmetry_vdw_refined 0.259 r_symmetry_vdw_other 0.238 r_symmetry_hbond_refined 0.223 r_xyhbond_nbd_refined 0.217 r_nbd_refined 0.205 r_nbd_other 0.201 r_nbtor_refined 0.177 r_chiral_restr 0.089 r_nbtor_other 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2122 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection SCALEPACK data scaling MOLREP phasing