6D06

Human ADAR2d E488Y mutant complexed with dsRNA containing an abasic site opposite the edited base


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZY7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1 M MES:NaOH pH 6.5, 14% PEG 20,000
Crystal Properties
Matthews coefficientSolvent content
2.657.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 174.68α = 90
b = 63.44β = 126.64
c = 132.06γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97946SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.5510697.40.0630.99815.273.4437329
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.6298.10.7230.7362.073.5

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 REPLACEMENTTHROUGHOUT1ZY72.55105.9635463186297.670.193340.190120.25518RANDOM64.39
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]
2.051.2-4.830.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.143
r_dihedral_angle_4_deg20.478
r_dihedral_angle_3_deg16.634
r_long_range_B_refined9.171
r_long_range_B_other9.171
r_dihedral_angle_1_deg7.166
r_scangle_other7.055
r_mcangle_it7.002
r_mcangle_other7.001
r_scbond_it4.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.143
r_dihedral_angle_4_deg20.478
r_dihedral_angle_3_deg16.634
r_long_range_B_refined9.171
r_long_range_B_other9.171
r_dihedral_angle_1_deg7.166
r_scangle_other7.055
r_mcangle_it7.002
r_mcangle_other7.001
r_scbond_it4.817
r_scbond_other4.815
r_mcbond_it4.698
r_mcbond_other4.695
r_angle_refined_deg1.739
r_angle_other_deg1.101
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms5760
Nucleic Acid Atoms967
Solvent Atoms48
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing