2QKB

Human RNase H catalytic domain mutant D210N in complex with 20-mer RNA/DNA hybrid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QK9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529415% PEG 3350, 0.1 M LiSO4, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4950.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.991α = 90
b = 109.991β = 90
c = 67.253γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.44090.80.0635.81867016949
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.490.4522.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2QK92.4401867016949168090.80.20760.255Random59.3
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it3.375
c_mcangle_it3.276
c_scbond_it2.262
c_mcbond_it1.879
c_angle_deg1.74222
c_bond_d0.012894
c_dihedral_angle_d
c_improper_angle_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2356
Nucleic Acid Atoms812
Solvent Atoms58
Heterogen Atoms18

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling