6MEA

Crystal structure of a Tylonycteris bat coronavirus HKU4 macrodomain in complex with adenosine diphosphate ribose (ADP-ribose)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DUSPDB entry 5DUS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29520-25% PEG3350, 0.1 M HEPES, pH 7.0-7.5, protein:ligand molar ratio 1:10
Crystal Properties
Matthews coefficientSolvent content
2.346.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.614α = 73.16
b = 41.642β = 88.29
c = 59.783γ = 88.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HSMirrors2017-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3539.8592.70.1210.1420.0740.9919.83.76331210
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)RedundancyNumber Unique Reflections (All)
11.351.3786.20.6570.7830.4210.66233.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 5DUS1.3533.5960045322592.870.14310.1420.1621RANDOM14.8
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]
0.030.110.040.110.02-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.368
r_sphericity_free19.902
r_dihedral_angle_4_deg14.602
r_dihedral_angle_3_deg11.224
r_sphericity_bonded8.143
r_dihedral_angle_1_deg6.312
r_rigid_bond_restr4.256
r_angle_refined_deg1.396
r_angle_other_deg0.931
r_chiral_restr0.398
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.368
r_sphericity_free19.902
r_dihedral_angle_4_deg14.602
r_dihedral_angle_3_deg11.224
r_sphericity_bonded8.143
r_dihedral_angle_1_deg6.312
r_rigid_bond_restr4.256
r_angle_refined_deg1.396
r_angle_other_deg0.931
r_chiral_restr0.398
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2426
Nucleic Acid Atoms
Solvent Atoms372
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing