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Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9-H275E with L-Trp non-covalently bound
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.85 298 13-21% PEG3350, 0.1 M HEPES pH 7.85
Crystal Properties Matthews coefficient Solvent content 2.26 45.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.402 α = 90 b = 82.658 β = 90 c = 322.255 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 9M 2021-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.033167 APS 21-ID-D
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
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 2.39 50 99.5 0.058 0.998 8.4 13.4 823988
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 2.39 2.45 99.5 1.548 0.488 0.8 14.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6AM8 2.39 46.695 61584 3098 99.305 0.229 0.2272 0.228 0.2714 0.2691 72.415
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] 1.735 5.909 -7.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_4_deg 16.624 r_dihedral_angle_3_deg 13.577 r_dihedral_angle_1_deg 6.822 r_lrange_it 2.913 r_lrange_other 2.913 r_mcangle_it 1.293 r_mcangle_other 1.293 r_angle_refined_deg 1.215 r_scangle_it 1.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_4_deg 16.624 r_dihedral_angle_3_deg 13.577 r_dihedral_angle_1_deg 6.822 r_lrange_it 2.913 r_lrange_other 2.913 r_mcangle_it 1.293 r_mcangle_other 1.293 r_angle_refined_deg 1.215 r_scangle_it 1.189 r_scangle_other 1.189 r_angle_other_deg 1.165 r_mcbond_it 0.746 r_mcbond_other 0.746 r_scbond_it 0.69 r_scbond_other 0.69 r_symmetry_xyhbond_nbd_refined 0.216 r_symmetry_nbd_refined 0.205 r_nbd_other 0.203 r_nbd_refined 0.176 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.152 r_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.04 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11078 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing