☰ Navigation Tabs
Crystal structure of a Tylonycteris bat coronavirus HKU4 macrodomain in complex with adenosine diphosphate ribose (ADP-ribose)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DUS PDB entry 5DUS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 20-25% PEG3350, 0.1 M HEPES, pH 7.0-7.5, protein:ligand molar ratio 1:10
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.614 α = 73.16 b = 41.642 β = 88.29 c = 59.783 γ = 88.25
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS Mirrors 2017-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1.35 39.85 92.7 0.121 0.142 0.074 0.991 9.8 3.7 63312 10
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 1.35 1.37 86.2 0.657 0.783 0.421 0.662 3 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 5DUS 1.35 33.59 60045 3225 92.87 0.1431 0.142 0.1422 0.1621 0.1617 RANDOM 14.8
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] 0.03 0.11 0.04 0.11 0.02 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.368 r_sphericity_free 19.902 r_dihedral_angle_4_deg 14.602 r_dihedral_angle_3_deg 11.224 r_sphericity_bonded 8.143 r_dihedral_angle_1_deg 6.312 r_rigid_bond_restr 4.256 r_angle_refined_deg 1.396 r_angle_other_deg 0.931 r_chiral_restr 0.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.368 r_sphericity_free 19.902 r_dihedral_angle_4_deg 14.602 r_dihedral_angle_3_deg 11.224 r_sphericity_bonded 8.143 r_dihedral_angle_1_deg 6.312 r_rigid_bond_restr 4.256 r_angle_refined_deg 1.396 r_angle_other_deg 0.931 r_chiral_restr 0.398 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2426 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing