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Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9 with Trp bound as E(Aex2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VM5
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 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.233 α = 90 b = 106.036 β = 90 c = 158.709 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 2017-01-13 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 1.83 40 99.2 0.036 0.999 11.5 7.3 121628
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 1.83 1.86 88.3 0.864 0.597 0.9 4.6
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 5VM5 1.83 40 115028 6031 98.62 0.20307 0.20155 0.2081 0.23141 0.2377 RANDOM 39.626
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] 3.44 -0.42 -3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.675 r_dihedral_angle_4_deg 15.191 r_dihedral_angle_3_deg 13.4 r_dihedral_angle_1_deg 5.957 r_long_range_B_refined 5.362 r_long_range_B_other 5.327 r_angle_refined_deg 1.074 r_angle_other_deg 0.779 r_mcangle_it 0.496 r_mcangle_other 0.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.675 r_dihedral_angle_4_deg 15.191 r_dihedral_angle_3_deg 13.4 r_dihedral_angle_1_deg 5.957 r_long_range_B_refined 5.362 r_long_range_B_other 5.327 r_angle_refined_deg 1.074 r_angle_other_deg 0.779 r_mcangle_it 0.496 r_mcangle_other 0.496 r_scangle_other 0.377 r_mcbond_other 0.274 r_mcbond_it 0.273 r_scbond_it 0.208 r_scbond_other 0.207 r_chiral_restr 0.059 r_bond_refined_d 0.005 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 11487 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing