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Aminodeoxychorismate synthase complex from Escherichia coli, with EDTA 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 2.68 54.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.965 α = 90 b = 109.446 β = 90 c = 178.859 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 2022-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976300 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 1.98 45.019 99.94 0.1027 0.999 16.7 13.2 108431
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 1.98 2.051 99.95 2.034 0.693 1.67 13.6
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 1.98 45.019 108431 5381 99.978 0.202 0.1999 0.2008 0.2388 0.2402 47.112
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] -2.75 3.332 -0.582
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.058 r_dihedral_angle_4_deg 20.337 r_dihedral_angle_3_deg 16.954 r_lrange_other 9.088 r_lrange_it 9.08 r_dihedral_angle_1_deg 7.443 r_scangle_it 7.258 r_scangle_other 7.252 r_mcangle_it 5.211 r_mcangle_other 5.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.058 r_dihedral_angle_4_deg 20.337 r_dihedral_angle_3_deg 16.954 r_lrange_other 9.088 r_lrange_it 9.08 r_dihedral_angle_1_deg 7.443 r_scangle_it 7.258 r_scangle_other 7.252 r_mcangle_it 5.211 r_mcangle_other 5.21 r_scbond_it 4.833 r_scbond_other 4.821 r_mcbond_it 3.815 r_mcbond_other 3.815 r_angle_refined_deg 1.522 r_angle_other_deg 1.292 r_symmetry_xyhbond_nbd_other 0.292 r_symmetry_nbd_refined 0.211 r_nbd_other 0.206 r_nbd_refined 0.196 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.162 r_nbtor_refined 0.159 r_ncsr_local_group_1 0.111 r_ncsr_local_group_2 0.11 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_refined 0.077 r_chiral_restr 0.073 r_metal_ion_refined 0.025 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10121 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing