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Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Asp at pH 4.5
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 4.5 293 0.1 M sodium acetate, pH 4.5, 25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.728 α = 90 b = 80.728 β = 90 c = 176.401 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 2019-08-09 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 2.13 39.4 97.2 0.061 0.028 0.995 27.3 5.7 71715
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 2.13 2.18 48.4 0.267 0.127 0.941 5.6 5.1
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 2.13 39.38 68787 2783 99.41 0.144 0.1418 0.1542 0.1982 0.2041 RANDOM 25.673
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 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.415 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 15.092 r_dihedral_angle_1_deg 7.428 r_angle_refined_deg 2.183 r_angle_other_deg 1.562 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.415 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 15.092 r_dihedral_angle_1_deg 7.428 r_angle_refined_deg 2.183 r_angle_other_deg 1.562 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9593 Nucleic Acid Atoms Solvent Atoms 870 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing