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Glutaminase subunit of aminodeoxychorismate synthase from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P00903-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 sodium formate, PEG3350, L-glutamine
Crystal Properties Matthews coefficient Solvent content 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.784 α = 90 b = 115.582 β = 101.062 c = 63.538 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 2022-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976200 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.82 42.423 98.54 0.3132 0.984 6.84 5.1 12448
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.921 98.31 1.486 0.513 1.75 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.82 42.423 12431 638 98.698 0.214 0.2109 0.2679 0.2743 51.505
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] 0.186 1.105 -1.185 0.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_4_deg 20.949 r_dihedral_angle_3_deg 20.864 r_lrange_it 11.96 r_lrange_other 11.96 r_dihedral_angle_1_deg 6.751 r_scangle_it 4.478 r_scangle_other 4.478 r_mcangle_other 4.477 r_mcangle_it 4.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_4_deg 20.949 r_dihedral_angle_3_deg 20.864 r_lrange_it 11.96 r_lrange_other 11.96 r_dihedral_angle_1_deg 6.751 r_scangle_it 4.478 r_scangle_other 4.478 r_mcangle_other 4.477 r_mcangle_it 4.474 r_scbond_it 2.599 r_scbond_other 2.597 r_mcbond_it 2.582 r_mcbond_other 2.571 r_angle_refined_deg 1.405 r_angle_other_deg 1.387 r_symmetry_xyhbond_nbd_refined 0.38 r_nbd_other 0.309 r_symmetry_nbd_refined 0.294 r_nbd_refined 0.217 r_symmetry_nbd_other 0.213 r_ncsr_local_group_3 0.18 r_symmetry_xyhbond_nbd_other 0.173 r_nbtor_refined 0.171 r_ncsr_local_group_2 0.17 r_ncsr_local_group_1 0.15 r_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_xyhbond_nbd_other 0.003 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4413 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing