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Crystal structure of Tylonycteris bat coronavirus HKU4 macrodomain in complex with nicotinamide adenine dinucleotide (NAD+)
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 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.607 α = 73.42 b = 41.561 β = 88.56 c = 59.912 γ = 88.43
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 PILATUS 2M Mirrors 2017-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.8 33.59 98.1 0.088 0.101 0.051 0.992 9.3 3.6 28245 10.3
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 1.8 1.84 82 0.166 0.206 0.118 0.905 4.3 2.4
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 1.8 33.59 26782 1461 98.1 0.1917 0.1895 0.1955 0.2323 0.2361 RANDOM 16.6
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] 0.15 0.09 0.05 0.03 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.038 r_dihedral_angle_4_deg 14.894 r_dihedral_angle_3_deg 14.164 r_dihedral_angle_1_deg 6.583 r_angle_refined_deg 1.365 r_angle_other_deg 0.917 r_chiral_restr 0.238 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.038 r_dihedral_angle_4_deg 14.894 r_dihedral_angle_3_deg 14.164 r_dihedral_angle_1_deg 6.583 r_angle_refined_deg 1.365 r_angle_other_deg 0.917 r_chiral_restr 0.238 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2417 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 88
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction PHASER phasing