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Crystal structure of a Tylonycteris bat coronavirus HKU4 macrodomain in complex with adenosine diphosphate glucose (ADP-glucose)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MEA PDB entry 6MEA
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 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.548 α = 73.04 b = 41.691 β = 88.37 c = 60.001 γ = 88.05
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 1.5 39.86 99.9 0.129 0.139 0.051 0.995 9.1 7.5 49739 16.1
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 1.5 1.53 100 1.284 1.382 0.508 0.721 1.9 7.4
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 6MEA 1.5 29.21 47290 2447 99.9 0.1747 0.1729 0.181 0.2086 0.2136 RANDOM 24.8
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] -0.2 -0.13 -0.02 0.18 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.112 r_sphericity_bonded 18.792 r_dihedral_angle_4_deg 15.052 r_dihedral_angle_3_deg 11.359 r_dihedral_angle_1_deg 6.728 r_angle_refined_deg 1.683 r_rigid_bond_restr 1.336 r_angle_other_deg 0.908 r_chiral_restr 0.11 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.112 r_sphericity_bonded 18.792 r_dihedral_angle_4_deg 15.052 r_dihedral_angle_3_deg 11.359 r_dihedral_angle_1_deg 6.728 r_angle_refined_deg 1.683 r_rigid_bond_restr 1.336 r_angle_other_deg 0.908 r_chiral_restr 0.11 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2426 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing