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Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB4D11 with Ser bound as E(Aex1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DW0
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 2.15 42.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.756 α = 90 b = 109.6 β = 90 c = 160.882 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 2015-07-23 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 1.63 40 99.9 0.035 0.999 12.2 6.7 186378
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 1.63 1.66 99.9 1.191 0.327 0.7 6.8
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 5DW0 1.63 40 175962 9239 99.21 0.20782 0.20651 0.2142 0.2328 0.2384 RANDOM 33.403
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] 0.68 1.86 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.436 r_dihedral_angle_4_deg 14.272 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 5.533 r_long_range_B_refined 3.788 r_long_range_B_other 3.725 r_angle_refined_deg 1.154 r_angle_other_deg 0.88 r_mcangle_it 0.555 r_mcangle_other 0.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.436 r_dihedral_angle_4_deg 14.272 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 5.533 r_long_range_B_refined 3.788 r_long_range_B_other 3.725 r_angle_refined_deg 1.154 r_angle_other_deg 0.88 r_mcangle_it 0.555 r_mcangle_other 0.555 r_scangle_other 0.355 r_mcbond_it 0.296 r_mcbond_other 0.296 r_scbond_it 0.18 r_scbond_other 0.18 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 11681 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing