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Crystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae co-crystallized with L-glutamine
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 2.19 43.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.291 α = 90 b = 170.915 β = 90 c = 160.344 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 2021-04-19 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 1.95 49.31 99.8 0.032 0.999 17.66 7.6 98481 40.29
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 1.95 2.02 98.6 0.797 0.616 1.33 7.9
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 1.95 47.11 93557 4924 99.82 0.21148 0.20996 0.213 0.24028 0.2404 RANDOM 66.309
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] 2.08 -1.27 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.563 r_dihedral_angle_4_deg 15.824 r_dihedral_angle_3_deg 14.947 r_dihedral_angle_1_deg 6.811 r_long_range_B_refined 3.589 r_long_range_B_other 3.581 r_angle_refined_deg 1.232 r_mcangle_it 1.145 r_mcangle_other 1.145 r_angle_other_deg 1.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.563 r_dihedral_angle_4_deg 15.824 r_dihedral_angle_3_deg 14.947 r_dihedral_angle_1_deg 6.811 r_long_range_B_refined 3.589 r_long_range_B_other 3.581 r_angle_refined_deg 1.232 r_mcangle_it 1.145 r_mcangle_other 1.145 r_angle_other_deg 1.132 r_scangle_other 1.018 r_mcbond_it 0.672 r_mcbond_other 0.672 r_scbond_it 0.598 r_scbond_other 0.594 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10102 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing