5QY6

PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry C05a


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
2.4449.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.748α = 90
b = 81.382β = 108.78
c = 92.808γ = 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
11.5144.5399.20.0590.0640.99911.726.8649406537.834
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)
11.511.60.9582.3382.5280.4150.436.5216146

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 SYNTHESISTHROUGHOUT1.5144.5394065495899.130.21950.218830.21953RANDOM35.892
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]
3.46-0.85-1.63-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.783
r_dihedral_angle_4_deg18.279
r_dihedral_angle_3_deg14.227
r_dihedral_angle_1_deg6.399
r_mcangle_it4.162
r_mcbond_it2.976
r_mcbond_other2.976
r_angle_refined_deg1.725
r_angle_other_deg1.399
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.783
r_dihedral_angle_4_deg18.279
r_dihedral_angle_3_deg14.227
r_dihedral_angle_1_deg6.399
r_mcangle_it4.162
r_mcbond_it2.976
r_mcbond_other2.976
r_angle_refined_deg1.725
r_angle_other_deg1.399
r_chiral_restr0.114
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4408
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms129

Software

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