5QYQ

PanDDA analysis group deposition -- Auto-refined data of Aar2/RNaseH for ground state model 06


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
2.4449.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.04α = 90
b = 81.638β = 108.27
c = 92.957γ = 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
11.6744.6681.50.0560.0610.99818.914.0675718333.766
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)
11.671.770.6020.1450.180.9529.481.6611892

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 SYNTHESISTHROUGHOUT1.6744.6657183298681.540.24210.240380.24213RANDOM37.792
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]
3.54-0.06-2.42-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.74
r_dihedral_angle_4_deg18.116
r_dihedral_angle_3_deg13.263
r_dihedral_angle_1_deg6.88
r_mcangle_it4.623
r_mcbond_it3.24
r_mcbond_other3.239
r_angle_refined_deg1.512
r_angle_other_deg1.336
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.74
r_dihedral_angle_4_deg18.116
r_dihedral_angle_3_deg13.263
r_dihedral_angle_1_deg6.88
r_mcangle_it4.623
r_mcbond_it3.24
r_mcbond_other3.239
r_angle_refined_deg1.512
r_angle_other_deg1.336
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4402
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms

Software

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