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Crystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae
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 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.67 α = 90 b = 171.405 β = 90 c = 160.838 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 2020-07-03 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 2.14 47.27 99.8 0.023 0.999 18.99 6.8 74670 52.19
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 2.14 2.22 98.1 0.581 0.64 1.29 6.7
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 2.14 47.26 70936 3734 99.76 0.22662 0.22429 0.2296 0.27161 0.2736 RANDOM 64.996
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] -1.62 5.66 -4.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.86 r_dihedral_angle_3_deg 15.396 r_dihedral_angle_4_deg 14.36 r_dihedral_angle_1_deg 6.319 r_long_range_B_refined 2.693 r_long_range_B_other 2.692 r_mcangle_it 1.506 r_mcangle_other 1.506 r_angle_refined_deg 1.197 r_scangle_other 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.86 r_dihedral_angle_3_deg 15.396 r_dihedral_angle_4_deg 14.36 r_dihedral_angle_1_deg 6.319 r_long_range_B_refined 2.693 r_long_range_B_other 2.692 r_mcangle_it 1.506 r_mcangle_other 1.506 r_angle_refined_deg 1.197 r_scangle_other 1.08 r_angle_other_deg 1.061 r_mcbond_it 0.827 r_mcbond_other 0.827 r_scbond_it 0.578 r_scbond_other 0.578 r_chiral_restr 0.038 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_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 10107 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing