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Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Asp at pH 5.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PGA PDB entry 4PGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 8% w/v Tacsimate, pH 5.0, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.21 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.958 α = 90 b = 80.958 β = 90 c = 176.819 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 PIXEL DECTRIS EIGER X 16M 2019-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.48 35.1 99.8 0.076 0.027 0.996 27.4 8.3 216530
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.52 98.3 0.737 0.349 0.732 2.2 4.9
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 PDB entry 4PGA 1.48 35.06 204714 3013 96.08 0.0881 0.0876 0.0945 0.1199 0.1247 RANDOM 16.109
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] -1.39 -1.39 2.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.586 r_sphericity_free 27.926 r_dihedral_angle_4_deg 15.016 r_dihedral_angle_3_deg 12.881 r_sphericity_bonded 12.245 r_dihedral_angle_1_deg 6.187 r_rigid_bond_restr 3.013 r_angle_refined_deg 1.89 r_angle_other_deg 1.072 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.586 r_sphericity_free 27.926 r_dihedral_angle_4_deg 15.016 r_dihedral_angle_3_deg 12.881 r_sphericity_bonded 12.245 r_dihedral_angle_1_deg 6.187 r_rigid_bond_restr 3.013 r_angle_refined_deg 1.89 r_angle_other_deg 1.072 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9620 Nucleic Acid Atoms Solvent Atoms 1244 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing