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1.50 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis in Complex with AMP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5US8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 Protein: 12.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 0.01mM ATP, 0.1mM Magnesium chloride;
Screen: Classics II (A3), 2M Ammonium sulfate, 0.1 Bis-Tris (pH 5.5); Cryo: Reservoir + 25% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.19 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.287 α = 90 b = 97.287 β = 90 c = 93.2 γ = 90
Symmetry Space Group P 42 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 C(111) 2017-06-20 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) Rrim I (All) 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 1.5 30 99.9 0.065 0.065 0.072 0.03 24.3 5.8 72217 -3 20.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.9 0.826 0.826 0.908 0.37 0.807 2.2 5.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5US8 1.5 29.59 68161 3684 99.87 0.15575 0.1545 0.1636 0.17856 0.1864 RANDOM 25.261
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] 0.84 0.84 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.885 r_dihedral_angle_4_deg 14.011 r_dihedral_angle_3_deg 10.567 r_long_range_B_refined 5.198 r_long_range_B_other 5.033 r_dihedral_angle_1_deg 4.38 r_scangle_other 3.286 r_scbond_it 2.163 r_scbond_other 2.147 r_mcangle_it 2.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.885 r_dihedral_angle_4_deg 14.011 r_dihedral_angle_3_deg 10.567 r_long_range_B_refined 5.198 r_long_range_B_other 5.033 r_dihedral_angle_1_deg 4.38 r_scangle_other 3.286 r_scbond_it 2.163 r_scbond_other 2.147 r_mcangle_it 2.097 r_mcangle_other 2.097 r_mcbond_it 1.35 r_mcbond_other 1.349 r_angle_refined_deg 1.341 r_angle_other_deg 0.45 r_chiral_restr 0.067 r_gen_planes_refined 0.044 r_gen_planes_other 0.04 r_bond_refined_d 0.008 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 3425 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing