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Crystal structure of DapD from Corynebacterium glutamicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FSX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 200, Li2SO4
Crystal Properties Matthews coefficient Solvent content 3.15 60.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.001 α = 90 b = 91.001 β = 90 c = 156.815 γ = 120
Symmetry Space Group P 63 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 270 2014-12-23 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 2.01 78.81 97.6 9.68 14.3 24585
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 3FSX 2.01 78.81 24585 1265 97.63 0.1785 0.1765 0.1874 0.2179 0.2243 RANDOM 33.703
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] 0.04 0.02 0.04 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.959 r_dihedral_angle_4_deg 22.173 r_dihedral_angle_3_deg 14.225 r_dihedral_angle_1_deg 7.18 r_mcangle_it 4.401 r_mcbond_it 3.139 r_mcbond_other 3.127 r_angle_refined_deg 1.894 r_angle_other_deg 1.054 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.959 r_dihedral_angle_4_deg 22.173 r_dihedral_angle_3_deg 14.225 r_dihedral_angle_1_deg 7.18 r_mcangle_it 4.401 r_mcbond_it 3.139 r_mcbond_other 3.127 r_angle_refined_deg 1.894 r_angle_other_deg 1.054 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2089 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling CNS phasing