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Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Sodium citrate tribasic, Sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.64 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.65 α = 90 b = 92.013 β = 90 c = 94.753 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 270 2016-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 2.4 94.76 96 26.88 4.7 36222
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 2.4 2.44
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 1HKV 2.4 23.708 36222 1898 95.52 0.1897 0.1864 0.1921 0.2531 0.2568 RANDOM 35.912
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] -0.63 0.76 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.499 r_dihedral_angle_4_deg 17.033 r_dihedral_angle_3_deg 15.097 r_dihedral_angle_1_deg 7.584 r_angle_refined_deg 1.725 r_angle_other_deg 1.025 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.499 r_dihedral_angle_4_deg 17.033 r_dihedral_angle_3_deg 15.097 r_dihedral_angle_1_deg 7.584 r_angle_refined_deg 1.725 r_angle_other_deg 1.025 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6652 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing HKL data reduction