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Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00015
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 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 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.26 α = 90 b = 105.26 β = 90 c = 160.65 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 1.62 46.17 99.9 0.088 0.091 0.999 14.12 11.39 130668
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 1.62 1.76 99.7 2.012 2.688 0.542 0.89
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 1.62 46.17 130599 6544 99.74 0.18061 0.1873 0.1881 0.1954 0.2032 RANDOM 32.075
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 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.663 r_long_range_B_refined 7.635 r_long_range_B_other 7.635 r_dihedral_angle_2_deg 6.989 r_scangle_other 6.133 r_dihedral_angle_1_deg 6.104 r_scbond_it 4.251 r_scbond_other 4.25 r_mcangle_it 3.67 r_mcangle_other 3.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.663 r_long_range_B_refined 7.635 r_long_range_B_other 7.635 r_dihedral_angle_2_deg 6.989 r_scangle_other 6.133 r_dihedral_angle_1_deg 6.104 r_scbond_it 4.251 r_scbond_other 4.25 r_mcangle_it 3.67 r_mcangle_other 3.67 r_mcbond_it 2.855 r_mcbond_other 2.849 r_angle_refined_deg 2.019 r_angle_other_deg 1.153 r_chiral_restr 0.103 r_bond_refined_d 0.018 r_gen_planes_other 0.015 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 5349 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction