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2.15 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein: 10.6 mg/ml, 0.01M Tris HCl (pH 8.3), ATP, Mg;
Screen: Classics II (G8), 0.2M Ammonium acetate, 0.1 HEPES (pH 7.5), 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.453 α = 90 b = 94.453 β = 90 c = 188.49 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 100 CCD MARMOSAIC 300 mm CCD C(111) 2017-02-02 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) R Sym I (Observed) Rpim I (All) 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 2.15 30 99.9 0.077 0.077 0.031 23.3 7.3 51703 -3 44.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 100 0.759 0.759 0.298 0.79 2.7 7.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1K92 2.15 29.46 49016 2519 99.91 0.15812 0.15605 0.20032 0.2267 RANDOM 52.267
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] -0.08 -0.04 -0.08 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.162 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_3_deg 10.281 r_long_range_B_refined 6.283 r_long_range_B_other 6.219 r_scangle_other 3.512 r_mcangle_other 2.96 r_mcangle_it 2.959 r_dihedral_angle_1_deg 2.854 r_scbond_it 2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.162 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_3_deg 10.281 r_long_range_B_refined 6.283 r_long_range_B_other 6.219 r_scangle_other 3.512 r_mcangle_other 2.96 r_mcangle_it 2.959 r_dihedral_angle_1_deg 2.854 r_scbond_it 2.28 r_scbond_other 2.28 r_mcbond_it 1.913 r_mcbond_other 1.912 r_angle_refined_deg 1.381 r_angle_other_deg 0.893 r_chiral_restr 0.085 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6934 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing