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Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00416
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 3.08 60.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.411 α = 90 b = 104.411 β = 90 c = 160.584 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) 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 46.06 99.8 0.134 0.999 10.85 11.4 138739
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.67 99.1 3.164 0.428 0.65
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 46.05 131841 6893 99.81 0.17533 0.17434 0.1839 0.19327 0.2 RANDOM 29.667
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 -0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.247 r_long_range_B_refined 8.123 r_long_range_B_other 8.013 r_scangle_other 6.664 r_dihedral_angle_2_deg 6.318 r_dihedral_angle_1_deg 6.03 r_scbond_it 4.649 r_scbond_other 4.648 r_mcangle_it 3.54 r_mcangle_other 3.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.247 r_long_range_B_refined 8.123 r_long_range_B_other 8.013 r_scangle_other 6.664 r_dihedral_angle_2_deg 6.318 r_dihedral_angle_1_deg 6.03 r_scbond_it 4.649 r_scbond_other 4.648 r_mcangle_it 3.54 r_mcangle_other 3.54 r_mcbond_it 2.671 r_mcbond_other 2.665 r_angle_refined_deg 1.896 r_angle_other_deg 1.031 r_chiral_restr 0.099 r_bond_refined_d 0.018 r_gen_planes_other 0.017 r_gen_planes_refined 0.014 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 5226 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data scaling DIMPLE phasing XDS data reduction