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Quinate dehydrogenase from Corynebacterium glutamicum in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NLO pdb entry 2nlo
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 293 1.6 M tri-sodium citrate, 0 up to 62.5 mM cobalt chloride, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.45 α = 90 b = 63.28 β = 94.46 c = 36.34 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 100 IMAGE PLATE MAR scanner 345 mm plate 2007-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8423 EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 10 93.1 0.065 0.065 34 3.8 147745 137551 17.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.04 85.9 0.615 0.615 2.05 3.1 14795
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2nlo 1 10 147745 137551 6770 93.1 0.16482 0.16482 0.16326 0.1745 0.19421 0.2025 Random 17.18
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.564 r_dihedral_angle_4_deg 16.513 r_dihedral_angle_3_deg 11.673 r_sphericity_free 9.91 r_sphericity_bonded 8.612 r_mcbond_other 6.118 r_dihedral_angle_1_deg 5.928 r_scangle_it 4.689 r_scbond_it 3.836 r_angle_other_deg 3.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.564 r_dihedral_angle_4_deg 16.513 r_dihedral_angle_3_deg 11.673 r_sphericity_free 9.91 r_sphericity_bonded 8.612 r_mcbond_other 6.118 r_dihedral_angle_1_deg 5.928 r_scangle_it 4.689 r_scbond_it 3.836 r_angle_other_deg 3.393 r_rigid_bond_restr 3.075 r_mcangle_it 3.056 r_mcbond_it 2.759 r_angle_refined_deg 1.764 r_symmetry_vdw_other 0.353 r_nbd_refined 0.254 r_nbd_other 0.23 r_symmetry_vdw_refined 0.188 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.106 r_nbtor_other 0.09 r_bond_refined_d 0.017 r_bond_other_d 0.013 r_gen_planes_other 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2075 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling