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Structure of the tryptophan synthase b-subunit from Pyroccus furiosus with b-methyltryptophan non-covalently bound
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 7.85 293 15-25% PEG3350, 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.1 41.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.819 α = 90 b = 107.705 β = 90 c = 160.061 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 PILATUS3 S 6M 2015-05-01 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) 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 1.8 40 99.4 0.999 12.8 13.5 125283
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 98.7 0.452 0.9 13.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5DW3 1.8 40 125283 6510 99.14 0.20571 0.20408 0.23768 0.2338 RANDOM 39.879
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] 3.23 -0.6 -2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.61 r_dihedral_angle_4_deg 14.753 r_dihedral_angle_3_deg 13.971 r_dihedral_angle_1_deg 6.066 r_long_range_B_refined 4.03 r_long_range_B_other 4.03 r_scangle_other 1.311 r_mcangle_it 1.213 r_mcangle_other 1.213 r_angle_refined_deg 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.61 r_dihedral_angle_4_deg 14.753 r_dihedral_angle_3_deg 13.971 r_dihedral_angle_1_deg 6.066 r_long_range_B_refined 4.03 r_long_range_B_other 4.03 r_scangle_other 1.311 r_mcangle_it 1.213 r_mcangle_other 1.213 r_angle_refined_deg 1.18 r_angle_other_deg 0.801 r_scbond_it 0.775 r_scbond_other 0.775 r_mcbond_it 0.702 r_mcbond_other 0.702 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 11723 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing