2E4L

Thermodynamic and Structural Analysis of Thermolabile RNase HI from Shewanella oneidensis MR-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.160.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.128α = 90
b = 77.128β = 90
c = 76.661γ = 90
Symmetry
Space GroupP 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2006-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90SPring-8BL44XU

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
11.83099.70.09623.54324518.2
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)
11.81.8698.20.5182.61

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 REPLACEMENTTHROUGHOUT2RN2227.221543280199.950.190170.188710.21851RANDOM23.202
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
r_dihedral_angle_3_deg20.164
r_scangle_it6.728
r_dihedral_angle_1_deg5.136
r_scbond_it4.401
r_mcangle_it2.949
r_angle_refined_deg2.314
r_mcbond_it1.728
r_angle_other_deg1.015
r_symmetry_hbond_refined0.544
r_symmetry_vdw_refined0.453
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg20.164
r_scangle_it6.728
r_dihedral_angle_1_deg5.136
r_scbond_it4.401
r_mcangle_it2.949
r_angle_refined_deg2.314
r_mcbond_it1.728
r_angle_other_deg1.015
r_symmetry_hbond_refined0.544
r_symmetry_vdw_refined0.453
r_chiral_restr0.29
r_nbd_refined0.256
r_nbd_other0.249
r_xyhbond_nbd_refined0.237
r_symmetry_vdw_other0.141
r_bond_refined_d0.035
r_gen_planes_refined0.013
r_gen_planes_other0.004
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1223
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms

Software

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