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Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB4D11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DVZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.85 298 15-25% PEG3350 and 0.1 M Na HEPES pH 7.85
Crystal Properties Matthews coefficient Solvent content 2.17 43.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.438 α = 90 b = 110.729 β = 90 c = 160.427 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 PILATUS 6M 2014-12-08 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) 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 1.93 40 99.7 0.023 0.998 15.4 6.7 114421
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 1.93 1.96 99.6 0.547 0.605 1.3 6.5
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 5DVZ 1.93 40 108623 5711 99.54 0.218 0.21604 0.2241 0.25527 0.2606 RANDOM 50.408
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] -0.11 2.95 -2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.823 r_dihedral_angle_4_deg 18.024 r_dihedral_angle_3_deg 13.777 r_dihedral_angle_1_deg 4.908 r_long_range_B_refined 4.403 r_long_range_B_other 4.392 r_angle_refined_deg 1.241 r_angle_other_deg 0.879 r_mcangle_it 0.789 r_mcangle_other 0.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.823 r_dihedral_angle_4_deg 18.024 r_dihedral_angle_3_deg 13.777 r_dihedral_angle_1_deg 4.908 r_long_range_B_refined 4.403 r_long_range_B_other 4.392 r_angle_refined_deg 1.241 r_angle_other_deg 0.879 r_mcangle_it 0.789 r_mcangle_other 0.788 r_scangle_other 0.583 r_mcbond_it 0.444 r_mcbond_other 0.444 r_scbond_it 0.32 r_scbond_other 0.319 r_chiral_restr 0.067 r_bond_refined_d 0.005 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 11501 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing