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Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Glu at pH 6.5
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 6.5 293 8% w/v Tacsimate, pH 6.5, 17% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.542 α = 90 b = 130.791 β = 117.82 c = 81.548 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2019-10-19 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 1.35 34.8 96.9 0.048 0.033 0.973 16 2.7 319520
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 1.35 1.39 94.5 0.547 0.402 0.579 2 2.6
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 1.35 34.76 302518 3218 92.64 0.1231 0.1229 0.1291 0.1494 0.1531 RANDOM 15.081
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] -2.49 4.68 2.92 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.69 r_sphericity_free 19.219 r_dihedral_angle_4_deg 14.565 r_dihedral_angle_3_deg 13.897 r_sphericity_bonded 6.786 r_dihedral_angle_1_deg 6.468 r_rigid_bond_restr 2.887 r_angle_refined_deg 2.121 r_angle_other_deg 1.163 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.69 r_sphericity_free 19.219 r_dihedral_angle_4_deg 14.565 r_dihedral_angle_3_deg 13.897 r_sphericity_bonded 6.786 r_dihedral_angle_1_deg 6.468 r_rigid_bond_restr 2.887 r_angle_refined_deg 2.121 r_angle_other_deg 1.163 r_chiral_restr 0.147 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9728 Nucleic Acid Atoms Solvent Atoms 1204 Heterogen Atoms 90
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing