5QY2

PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry A12b


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529319% (w/v) Peg 4000, 3% (v/v) DMSO, 0.1M Tris-HCl pH 8.5, 0.2M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.4649.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.522α = 90
b = 82.031β = 108.83
c = 93.961γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.827MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.3643.7797.50.0790.0860.9989.996.71112721139.405
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.690.9132.6812.9020.3550.556.1913748

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.3643.77127211657897.910.21790.217070.2179RANDOM28.516
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]
1.09-0.07-1.150.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.311
r_dihedral_angle_4_deg17.302
r_dihedral_angle_3_deg13.577
r_dihedral_angle_1_deg6.34
r_mcangle_it3.588
r_mcbond_it2.456
r_mcbond_other2.456
r_angle_refined_deg1.712
r_angle_other_deg1.462
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.311
r_dihedral_angle_4_deg17.302
r_dihedral_angle_3_deg13.577
r_dihedral_angle_1_deg6.34
r_mcangle_it3.588
r_mcbond_it2.456
r_mcbond_other2.456
r_angle_refined_deg1.712
r_angle_other_deg1.462
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4562
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms62

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
PHENIXrefinement