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Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00259
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 3.1 60.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.907 α = 90 b = 104.907 β = 90 c = 160.338 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 1.58 46.07 99.9 0.087 0.096 0.999 14.73 11.3 139890
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 1.58 1.72 1.885 2.536 0.582 0.9
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 1.58 46.07 132916 6964 99.84 0.20859 0.20789 0.214 0.22126 0.2261 RANDOM 29.693
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] -0.02 -0.01 -0.02 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.396 r_long_range_B_refined 7.166 r_long_range_B_other 7.166 r_scangle_other 5.948 r_dihedral_angle_1_deg 5.786 r_dihedral_angle_2_deg 5.675 r_scbond_it 4.18 r_scbond_other 4.179 r_mcangle_it 3.869 r_mcangle_other 3.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.396 r_long_range_B_refined 7.166 r_long_range_B_other 7.166 r_scangle_other 5.948 r_dihedral_angle_1_deg 5.786 r_dihedral_angle_2_deg 5.675 r_scbond_it 4.18 r_scbond_other 4.179 r_mcangle_it 3.869 r_mcangle_other 3.869 r_mcbond_it 2.837 r_mcbond_other 2.829 r_angle_refined_deg 1.803 r_angle_other_deg 1.024 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_gen_planes_other 0.015 r_gen_planes_refined 0.012 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 5434 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data scaling DIMPLE phasing XDS data reduction