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Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00065 covalently linked to the catalytic lysine (K329)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.025-0.125 mM carboxylic acid mix, 30-60% precipitant mix (MPD, PEG 1000, PEG 3350), 100 mM Tris-Bicine pH = 8.5
Crystal Properties Matthews coefficient Solvent content 3.13 60.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.34 α = 90 b = 105.34 β = 90 c = 160.364 γ = 120
Symmetry Space Group P 32 2 1
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 EIGER2 X 16M 2021-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.52 46.12 99.9 0.09 0.095 0.999 13.6 11.44 158297 35.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 99.6 3.198 3.95 0.287 0.46
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.52 46.12 150450 7840 99.9 0.18711 0.18616 0.1992 0.20437 0.2122 RANDOM 32.815
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.494 r_long_range_B_refined 7.222 r_long_range_B_other 7.222 r_dihedral_angle_2_deg 6.524 r_dihedral_angle_1_deg 6.219 r_scangle_other 5.977 r_scbond_it 4.116 r_scbond_other 4.115 r_mcangle_other 3.977 r_mcangle_it 3.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.494 r_long_range_B_refined 7.222 r_long_range_B_other 7.222 r_dihedral_angle_2_deg 6.524 r_dihedral_angle_1_deg 6.219 r_scangle_other 5.977 r_scbond_it 4.116 r_scbond_other 4.115 r_mcangle_other 3.977 r_mcangle_it 3.976 r_mcbond_it 2.975 r_mcbond_other 2.969 r_angle_refined_deg 1.825 r_angle_other_deg 1.093 r_chiral_restr 0.099 r_bond_refined_d 0.018 r_gen_planes_other 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.002 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 5355 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data scaling DIMPLE phasing XDS data reduction