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TxGH116 complex with a beta-d-Arabinofuranose-configured cyclitol aziridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 PEG 3000, ammonium sulfate, MES
Crystal Properties Matthews coefficient Solvent content 2.17 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.723 α = 90 b = 53.919 β = 90 c = 83.165 γ = 90
Symmetry Space Group P 21 21 2
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 2025-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 53.92 100 0.167 0.181 0.069 0.996 10.2 12.9 81586
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 1.925 2.087 0.801 0.633 1.3 13.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 51.597 81291 4111 99.709 0.185 0.1831 0.1831 0.2124 0.2125 RANDOM 26.349
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] 1.157 -0.523 -0.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.101 r_dihedral_angle_3_deg 12.701 r_dihedral_angle_1_deg 7.094 r_dihedral_angle_2_deg 6.321 r_lrange_it 4.654 r_scangle_it 2.83 r_scbond_it 2.112 r_mcangle_it 2.06 r_angle_refined_deg 1.875 r_mcbond_it 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.101 r_dihedral_angle_3_deg 12.701 r_dihedral_angle_1_deg 7.094 r_dihedral_angle_2_deg 6.321 r_lrange_it 4.654 r_scangle_it 2.83 r_scbond_it 2.112 r_mcangle_it 2.06 r_angle_refined_deg 1.875 r_mcbond_it 1.48 r_nbtor_refined 0.317 r_nbd_refined 0.209 r_symmetry_nbd_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.15 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.131 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6125 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data reduction gemmi data extraction Aimless data scaling DIALS data reduction gemmi data extraction PHASER phasing