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2.5 Angstrom Resolution Crystal Structure of 3-Dehydroquinate Synthase (aroB) from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 3.5 mGr/mL 0.01M Tris-HCL pH 8.3, 1mM Dehydroquinate (DHQ); Screen: Classics II (B6), 0.49M Sodium phosphate, 0.91M Potassium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.14 α = 90 b = 80.14 β = 90 c = 262.965 γ = 90
Symmetry Space Group P 43 21 2
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 MARMOSAIC 300 mm CCD Beryllium lenses 2010-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.5 30 100 0.078 19.7 5.5 30764 30764 -3 52.5
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) 2.5 2.54 100 0.517 2.7 5.6 1480
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 3CLH 2.5 29.62 29101 29101 1549 99.88 0.18379 0.18379 0.18168 0.1866 0.2228 0.2226 RANDOM 41.904
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] 2.18 2.18 -4.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.356 r_dihedral_angle_4_deg 9.803 r_dihedral_angle_3_deg 9.141 r_scangle_it 4.033 r_scbond_it 2.484 r_dihedral_angle_1_deg 2.198 r_mcangle_it 1.62 r_angle_refined_deg 1.295 r_mcbond_it 0.845 r_angle_other_deg 0.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.356 r_dihedral_angle_4_deg 9.803 r_dihedral_angle_3_deg 9.141 r_scangle_it 4.033 r_scbond_it 2.484 r_dihedral_angle_1_deg 2.198 r_mcangle_it 1.62 r_angle_refined_deg 1.295 r_mcbond_it 0.845 r_angle_other_deg 0.823 r_mcbond_other 0.17 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5407 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 116
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling