6R0R

Getah virus macro domain in complex with ADPr covalently bond to Cys34


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6QZU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.9293Imidazole-Malate pH 5.9, 38% PEG 4K, 3 mM ADPr, 3 mM Aspartic acid
Crystal Properties
Matthews coefficientSolvent content
2.1442.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.011α = 90
b = 46.801β = 104.16
c = 51.004γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2017-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.98005SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.4537.3799.90.0430.0430.0510.0270.99920.66.62602617.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.471000.7490.7490.8950.4840.7752.16.5

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 REPLACEMENTTHROUGHOUT6QZU1.4537.3724542148399.860.171010.169460.19667RANDOM19.46
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]
-0.67-0.070.320.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.148
r_dihedral_angle_4_deg20.463
r_dihedral_angle_3_deg10.896
r_scangle_other9.451
r_long_range_B_refined9.419
r_long_range_B_other9.416
r_scbond_it9.051
r_scbond_other9.046
r_dihedral_angle_1_deg5.983
r_mcangle_other3.516
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.148
r_dihedral_angle_4_deg20.463
r_dihedral_angle_3_deg10.896
r_scangle_other9.451
r_long_range_B_refined9.419
r_long_range_B_other9.416
r_scbond_it9.051
r_scbond_other9.046
r_dihedral_angle_1_deg5.983
r_mcangle_other3.516
r_mcangle_it3.462
r_mcbond_it3.301
r_mcbond_other2.881
r_angle_refined_deg1.583
r_angle_other_deg1.551
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1210
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing