5USE

5-Se-T4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G8U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M MES pH 6.5, 12%(w/v) PEG 20000
Crystal Properties
Matthews coefficientSolvent content
2.3547.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.912α = 90
b = 37.56β = 96.17
c = 62.258γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.735099.80.03953.7619601

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 REPLACEMENTTHROUGHOUT2g8u1.7330.94918567103499.690.194190.191960.23398RANDOM27.801
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.082
r_dihedral_angle_4_deg18.317
r_dihedral_angle_3_deg14.099
r_long_range_B_other6.409
r_long_range_B_refined6.406
r_dihedral_angle_1_deg6.384
r_scangle_other5.29
r_scbond_it3.679
r_scbond_other3.677
r_mcangle_other3.493
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.082
r_dihedral_angle_4_deg18.317
r_dihedral_angle_3_deg14.099
r_long_range_B_other6.409
r_long_range_B_refined6.406
r_dihedral_angle_1_deg6.384
r_scangle_other5.29
r_scbond_it3.679
r_scbond_other3.677
r_mcangle_other3.493
r_mcangle_it3.492
r_mcbond_it2.614
r_mcbond_other2.584
r_angle_refined_deg2.039
r_angle_other_deg1.245
r_chiral_restr0.132
r_bond_refined_d0.021
r_bond_other_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms246
Solvent Atoms32
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing