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Tryptophan Synthase beta-subunit from Pyrococcus furiosus with L-threonine non-covalently bound in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.85 298.15 15-25% PEG3350, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.28 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.718 α = 90 b = 112.367 β = 90 c = 160.31 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 PSI PILATUS 6M 2015-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.54 40 98.9 0.064 1 19.4 9.8 214599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 78.1 1.403 1.3 5.5
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 5DW3 1.54 40 214599 11224 97.66 0.17607 0.17508 0.187 0.19486 0.2055 RANDOM 25.067
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] 0.54 0.38 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.655 r_dihedral_angle_4_deg 17.731 r_dihedral_angle_3_deg 12.89 r_dihedral_angle_1_deg 6.175 r_long_range_B_refined 5.497 r_long_range_B_other 5.451 r_scangle_other 1.84 r_angle_refined_deg 1.176 r_scbond_it 1.15 r_scbond_other 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.655 r_dihedral_angle_4_deg 17.731 r_dihedral_angle_3_deg 12.89 r_dihedral_angle_1_deg 6.175 r_long_range_B_refined 5.497 r_long_range_B_other 5.451 r_scangle_other 1.84 r_angle_refined_deg 1.176 r_scbond_it 1.15 r_scbond_other 1.15 r_mcangle_it 1.139 r_mcangle_other 1.139 r_angle_other_deg 0.705 r_mcbond_it 0.695 r_mcbond_other 0.695 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 11797 Nucleic Acid Atoms Solvent Atoms 842 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing