7KFN

Structure of Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA containing a 2'-deoxy Benner's Base Z opposite the edited base


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6D06 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298100 mM MES:NaOH pH 6.5, 18% PEG 20,000
Crystal Properties
Matthews coefficientSolvent content
2.7654.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 172.024α = 90
b = 63.612β = 126.77
c = 132.149γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

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
12.5105.8699.40.110.1270.0630.9938.73.839692
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)
12.52.699.10.6130.7140.360.7143.8

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 REPLACEMENTTHROUGHOUT6D062.568.9937774190799.270.17330.17070.2256RANDOM46.536
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.423
r_dihedral_angle_4_deg17.705
r_dihedral_angle_3_deg16.873
r_dihedral_angle_1_deg7.541
r_angle_refined_deg1.58
r_angle_other_deg1.267
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.423
r_dihedral_angle_4_deg17.705
r_dihedral_angle_3_deg16.873
r_dihedral_angle_1_deg7.541
r_angle_refined_deg1.58
r_angle_other_deg1.267
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5804
Nucleic Acid Atoms977
Solvent Atoms252
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata processing
PHASERphasing
Aimlessdata reduction