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Crystal Structure of Argininosuccinate synthase from Legionella pneumophila Philadelphia 1 in complex with ANPPNP and a substrate analogue Arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XNQ apo structure, pdb entry 6XNQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 Microlytic MCSG1 screen C5: 200mM MgOAc2, 20% (w/V) PEG 3350: LepnA.00809.a.B1.PS38414 + 3.5mM of each AMPPNP, Arginine, MgCl2: tray 316695 c5: cryo: 20% EG + 3.5mm AmPPNP and Arginine: puck iyy7-9
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.23 α = 90 b = 103.54 β = 96.005 c = 147.41 γ = 90
Symmetry Space Group C 1 2 1
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 RAYONIX MX-300 Beryllium Lenses 2020-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.85 50 99.2 0.075 0.085 0.998 14.7 4.668 154253 27.862
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 98.8 0.589 0.665 0.856 3.17 4.681
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE apo structure, pdb entry 6XNQ 1.85 48.87 1.35 154171 2025 99.16 0.1571 0.1567 0.1568 0.1901 0.1887 0 24
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 f_dihedral_angle_d 13.8536 f_angle_d 0.9271 f_chiral_restr 0.0608 f_bond_d 0.0087 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11971 Nucleic Acid Atoms Solvent Atoms 1590 Heterogen Atoms 260
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing Coot model building