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Crystal structure of Aspergillus nidulans 3-dehydroquinate synthase (AnDHQS) in complex with Zn2+ and NAD+, at 1.7D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 PEG 3350, lithium sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.02 α = 90 b = 104.51 β = 90 c = 177.44 γ = 90
Symmetry Space Group C 2 2 21
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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.933 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 30 0.123 13.67 7.2 90933 -1.5 17.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.73 94.6 0.735 1.55 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1NVE 1.7 30 -1.5 90933 90933 99.6 0.25 0.25 0.195 0.1946 0.25 0.2485 random 24.9
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] -2.49 2.17 0.32
RMS Deviations Key Refinement Restraint Deviation o_dihedral_angle_d 21.3 o_angle_d 1.2 o_improper_angle_d 0.78 o_bond_d 0.006 o_bond_d_na o_bond_d_prot o_angle_d_na o_angle_d_prot o_angle_deg o_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation o_dihedral_angle_d 21.3 o_angle_d 1.2 o_improper_angle_d 0.78 o_bond_d 0.006 o_bond_d_na o_bond_d_prot o_angle_d_na o_angle_d_prot o_angle_deg o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d_na o_dihedral_angle_d_prot o_improper_angle_d_na o_improper_angle_d_prot o_mcbond_it o_mcangle_it o_scbond_it o_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5790 Nucleic Acid Atoms Solvent Atoms 1307 Heterogen Atoms 90
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing