4IBN

Crystal structure of LC9-RNase H1, a type 1 RNase H with the type 2 active-site motif


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5277100mM Tris-HCl, 200mM MgCl2.6H2O, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.7128.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.633α = 90
b = 39.913β = 102.64
c = 50.254γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 65002012-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.625099.20.0770.07743.64813.720537-3
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)
11.621.6596.20.34913.71000

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-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2EHG1.6249.042053720485103999.190.1790.1790.17710.2152RANDOM25.5324
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]
0.930.890.39-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.563
r_dihedral_angle_4_deg16.451
r_dihedral_angle_3_deg14.593
r_dihedral_angle_1_deg7.372
r_scangle_it6.862
r_scbond_it4.343
r_mcangle_it2.991
r_mcbond_it1.852
r_angle_refined_deg1.022
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.563
r_dihedral_angle_4_deg16.451
r_dihedral_angle_3_deg14.593
r_dihedral_angle_1_deg7.372
r_scangle_it6.862
r_scbond_it4.343
r_mcangle_it2.991
r_mcbond_it1.852
r_angle_refined_deg1.022
r_chiral_restr0.088
r_gen_planes_refined0.017
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1613
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection