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Engineered TrpB from Pyrococcus furiosus, PfTrpB7E6 with (2S,3R)-ethylserine bound as the amino-acrylate
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 7.85 293 14% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.222 α = 90 b = 109.297 β = 90 c = 159.928 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 2016-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.19499 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.75 40 100 0.085 0.1 0.05 0.981 8.2 4.1 148965
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 1.115 1.277 0.613 0.753 4.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5VM5 1.75 40 141404 7409 99.89 0.2363 0.235 0.2611 0.261 RANDOM 36.149
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 1.36 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.397 r_dihedral_angle_3_deg 12.979 r_dihedral_angle_4_deg 12.703 r_dihedral_angle_1_deg 5.452 r_angle_refined_deg 1.115 r_angle_other_deg 0.767 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.397 r_dihedral_angle_3_deg 12.979 r_dihedral_angle_4_deg 12.703 r_dihedral_angle_1_deg 5.452 r_angle_refined_deg 1.115 r_angle_other_deg 0.767 r_chiral_restr 0.059 r_bond_refined_d 0.006 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 11373 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 57
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction