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Aminodeoxychorismate synthase complex from Escherichia coli
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 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.505 α = 90 b = 108.326 β = 90 c = 179.758 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 2.45 46.434 99.88 0.1465 0.998 11.91 13.4 57850
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 2.45 2.538 99.79 1.699 0.806 1.79 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 2.45 46.434 57849 2342 99.964 0.206 0.2042 0.2069 0.2537 0.2162 57.944
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] -4.595 6.145 -1.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.985 r_dihedral_angle_3_deg 19.475 r_dihedral_angle_4_deg 17.557 r_lrange_other 11.605 r_lrange_it 11.603 r_scangle_it 7.386 r_scangle_other 7.385 r_dihedral_angle_1_deg 7.23 r_mcangle_it 6.309 r_mcangle_other 6.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.985 r_dihedral_angle_3_deg 19.475 r_dihedral_angle_4_deg 17.557 r_lrange_other 11.605 r_lrange_it 11.603 r_scangle_it 7.386 r_scangle_other 7.385 r_dihedral_angle_1_deg 7.23 r_mcangle_it 6.309 r_mcangle_other 6.308 r_scbond_it 4.685 r_scbond_other 4.682 r_mcbond_it 4.185 r_mcbond_other 4.185 r_angle_refined_deg 1.504 r_angle_other_deg 1.269 r_symmetry_xyhbond_nbd_other 0.316 r_symmetry_nbd_refined 0.315 r_metal_ion_refined 0.292 r_nbd_other 0.242 r_symmetry_xyhbond_nbd_refined 0.214 r_nbd_refined 0.197 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.155 r_ncsr_local_group_1 0.126 r_ncsr_local_group_2 0.109 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10128 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing