☰ Navigation Tabs
Crystal structure of DapD in complex with succinyl-CoA 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 3.97 69.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.457 α = 90 b = 92.457 β = 90 c = 282.341 γ = 120
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 2015-05-19 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 1.8 94.11 99.17 61.68 10.5 41214
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 1.8 94.11 41214 2093 99.17 0.158 0.1566 0.1705 0.1874 0.1962 RANDOM 23.175
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] 0.22 0.11 0.22 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.128 r_dihedral_angle_4_deg 20.274 r_dihedral_angle_3_deg 11.935 r_dihedral_angle_1_deg 6.524 r_mcangle_it 3.288 r_angle_refined_deg 2.424 r_mcbond_it 2.416 r_mcbond_other 2.414 r_angle_other_deg 1.137 r_chiral_restr 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.128 r_dihedral_angle_4_deg 20.274 r_dihedral_angle_3_deg 11.935 r_dihedral_angle_1_deg 6.524 r_mcangle_it 3.288 r_angle_refined_deg 2.424 r_mcbond_it 2.416 r_mcbond_other 2.414 r_angle_other_deg 1.137 r_chiral_restr 0.148 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2052 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 55
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