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Aminodeoxychorismate synthase complex from Escherichia coli, with glutamine added
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 MES, magnesium sulfate heptahydrate, glycerol
Crystal Properties Matthews coefficient Solvent content 2.64 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.403 α = 90 b = 109.912 β = 90 c = 174.278 γ = 90
Symmetry Space Group P 21 21 21
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 2021-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.968000 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 1.86 46.929 99.96 0.09922 0.998 16.67 13.3 128415
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 1.86 1.926 99.98 1.09 0.853 2.63 13.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.86 46.929 128407 6391 99.976 0.168 0.1668 0.1672 0.2014 0.2021 34.304
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] -1.265 2.117 -0.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.068 r_dihedral_angle_4_deg 18.098 r_dihedral_angle_3_deg 14.395 r_lrange_it 7.804 r_lrange_other 7.801 r_dihedral_angle_1_deg 7.042 r_scangle_it 6.41 r_scangle_other 6.408 r_scbond_it 4.5 r_scbond_other 4.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.068 r_dihedral_angle_4_deg 18.098 r_dihedral_angle_3_deg 14.395 r_lrange_it 7.804 r_lrange_other 7.801 r_dihedral_angle_1_deg 7.042 r_scangle_it 6.41 r_scangle_other 6.408 r_scbond_it 4.5 r_scbond_other 4.495 r_mcangle_it 4.17 r_mcangle_other 4.169 r_mcbond_it 3.203 r_mcbond_other 3.203 r_angle_refined_deg 1.564 r_angle_other_deg 1.396 r_nbd_other 0.266 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.182 r_symmetry_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.165 r_ncsr_local_group_1 0.125 r_ncsr_local_group_2 0.088 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.034 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10139 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms 198
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing