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Crystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae with chorismate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other PDB 1QDL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 51% (v/v) Tacsimate, 0.1 M Bis-tris propane (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.289 α = 90 b = 170.784 β = 90 c = 162.079 γ = 90
Symmetry Space Group C 2 2 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 2021-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.03 47.48 99.9 0.022 1 20.87 7.6 88867 45.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.1 99.8 0.618 1 1.41 7.2
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 1QDL 2.03 47.47 84467 4446 99.87 0.22077 0.21771 0.2326 0.2794 0.2921 RANDOM 63.689
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] -1.1 8.03 -6.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.538 r_dihedral_angle_1_deg 6.387 r_long_range_B_refined 3.982 r_long_range_B_other 3.978 r_dihedral_angle_2_deg 3.448 r_mcangle_it 3.125 r_mcangle_other 3.125 r_scangle_other 2.724 r_mcbond_it 2.177 r_mcbond_other 2.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.538 r_dihedral_angle_1_deg 6.387 r_long_range_B_refined 3.982 r_long_range_B_other 3.978 r_dihedral_angle_2_deg 3.448 r_mcangle_it 3.125 r_mcangle_other 3.125 r_scangle_other 2.724 r_mcbond_it 2.177 r_mcbond_other 2.176 r_scbond_it 1.973 r_scbond_other 1.973 r_rigid_bond_restr 1.076 r_angle_refined_deg 0.785 r_angle_other_deg 0.282 r_chiral_restr 0.039 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10017 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing