☰ Navigation Tabs
Crystal structure of 3-dehydroquinate synthase (DHQS)from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NRX PDB ENTRY 1NRX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20mM NAD, 3.5M NaFormate, 0.1M Tris-HCl (pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 58.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.294 α = 90 b = 158.294 β = 90 c = 97.387 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 IMAGE PLATE RIGAKU RAXIS IV++ 2006-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 2.4 79.31 99.7 35600 35489
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49
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 (All) 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 1NRX 2.4 30 35489 1821 0.21 0.207 0.2777 0.258 0.3024 RANDOM
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 33.92 r_dihedral_angle_1_deg 7.378 r_angle_refined_deg 1.52 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.109 r_symmetry_hbond_refined 0.066 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.92 r_dihedral_angle_1_deg 7.378 r_angle_refined_deg 1.52 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.109 r_symmetry_hbond_refined 0.066 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4902 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 90
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling