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The aminoacrylate form of the beta-Q114A mutant Tryptophan Synthase at 1.50 Angstrom resolution with cesium ion at the metal coordination site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VFD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 298 50 mM Bicine-CsOH, 10% PEG 8,000, 4 mM Spermine, pH 7.6
Crystal Properties Matthews coefficient Solvent content 2.33 0.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.622 α = 90 b = 59.92 β = 94.87 c = 67.416 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS 6M 2020-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.499 90.982 98.4 0.069 0.069 0.08 0.031 10.1 6.6 114154
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 97.6 0.478 0.478 0.559 0.22 1.3 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6VFD 1.5 39.28 107867 5768 97.8 0.1796 0.1776 0.2166 0.2326 RANDOM 39.64
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] -0.98 -0.21 1.15 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_4_deg 18.649 r_dihedral_angle_3_deg 13.369 r_rigid_bond_restr 9.45 r_dihedral_angle_1_deg 6.258 r_angle_refined_deg 1.537 r_chiral_restr 0.103 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4852 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 96
Software Software Software Name Purpose xia2 data reduction SCALA data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction