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Unliganded form of hydroxyamidotransferase TsnB9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 30% (w/v) PEG 8,000, 0.2 M ammonium sulfate, and 0.1 M sodium cacodylate trihydrate (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.68 α = 101.153 b = 76.57 β = 114.435 c = 82.14 γ = 109.556
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 2M-F 2020-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.72 50 91.8 0.099 0.986 6.42 1.9 64632
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.72 2.79 0.615 0.702 1.14
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold model 2.72 33.611 33710 1691 96.207 0.268 0.2661 0.2664 0.2937 0.299 35.863
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] 0.407 0.538 -1.021 3.152 0.37 -1.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.749 r_dihedral_angle_3_deg 13.758 r_dihedral_angle_4_deg 13.594 r_dihedral_angle_1_deg 5.091 r_lrange_it 1.363 r_lrange_other 1.363 r_angle_refined_deg 1.187 r_angle_other_deg 1.086 r_mcangle_it 0.389 r_mcangle_other 0.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.749 r_dihedral_angle_3_deg 13.758 r_dihedral_angle_4_deg 13.594 r_dihedral_angle_1_deg 5.091 r_lrange_it 1.363 r_lrange_other 1.363 r_angle_refined_deg 1.187 r_angle_other_deg 1.086 r_mcangle_it 0.389 r_mcangle_other 0.389 r_mcbond_it 0.204 r_mcbond_other 0.204 r_scangle_it 0.166 r_scangle_other 0.165 r_nbd_refined 0.16 r_symmetry_nbd_other 0.157 r_nbtor_refined 0.146 r_nbd_other 0.146 r_xyhbond_nbd_refined 0.109 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbd_refined 0.097 r_symmetry_nbtor_other 0.073 r_scbond_it 0.066 r_scbond_other 0.063 r_chiral_restr 0.032 r_symmetry_xyhbond_nbd_other 0.004 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8691 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing