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Crystal Structure of the Quinate Dehydrogenase from Corynebacterium glutamicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NVT PDB ENTRY 1NVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.784 α = 90 b = 63.021 β = 92.24 c = 35.527 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.843 EMBL/DESY, HAMBURG BW7B
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 1.6 7.99 29404
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 PDB ENTRY 1NVT 1.643 7.99 29404 1526 97.64 0.149 0.14812 0.1561 0.16543 0.1721 RANDOM 14.399
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] 0.18 -0.04 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.942 r_dihedral_angle_4_deg 19.444 r_dihedral_angle_3_deg 11.536 r_dihedral_angle_1_deg 5.709 r_scangle_it 4.162 r_scbond_it 3.022 r_mcangle_it 2.626 r_mcbond_it 2.391 r_angle_refined_deg 1.135 r_angle_other_deg 0.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.942 r_dihedral_angle_4_deg 19.444 r_dihedral_angle_3_deg 11.536 r_dihedral_angle_1_deg 5.709 r_scangle_it 4.162 r_scbond_it 3.022 r_mcangle_it 2.626 r_mcbond_it 2.391 r_angle_refined_deg 1.135 r_angle_other_deg 0.845 r_mcbond_other 0.596 r_symmetry_vdw_other 0.335 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.199 r_nbd_other 0.195 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.145 r_symmetry_vdw_refined 0.094 r_nbtor_other 0.085 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2067 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing