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Crystal structure of tolypothrichol synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.5 M Ammonium sulfate
0.1 M Sodium citrate tribasic dihydrate, pH 5.6
1.0 M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 1.86 33.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.155 α = 90 b = 55.77 β = 90.75 c = 57.66 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 S 6M 2023-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.76 49.2 99.2 0.03 0.036 0.02 0.999 12.8 3.3 30831
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 1.76 1.79 99.9 0.508 0.612 0.337 0.826 1.8
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 AlphaFold 1.76 49.2 29269 1546 99.15 0.18139 0.17913 0.22378 0.2421 RANDOM 35.276
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] -0.38 2.46 -0.64 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.067 r_dihedral_angle_2_deg 13.267 r_long_range_B_other 8.656 r_long_range_B_refined 8.654 r_scangle_other 7.753 r_dihedral_angle_1_deg 6.843 r_scbond_other 5.853 r_scbond_it 5.848 r_mcangle_it 5.125 r_mcangle_other 5.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.067 r_dihedral_angle_2_deg 13.267 r_long_range_B_other 8.656 r_long_range_B_refined 8.654 r_scangle_other 7.753 r_dihedral_angle_1_deg 6.843 r_scbond_other 5.853 r_scbond_it 5.848 r_mcangle_it 5.125 r_mcangle_other 5.124 r_mcbond_it 4.134 r_mcbond_other 4.132 r_angle_refined_deg 2.385 r_angle_other_deg 0.801 r_chiral_restr 0.127 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2631 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing