4WA8

Methanopyrus Kandleri FEN-1 nuclease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5290PEG4000, Tris-HCL, sodium chloride, calcium chloride
Crystal Properties
Matthews coefficientSolvent content
2.1843.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.331α = 90
b = 86.193β = 90
c = 147.617γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
12.274.4396.40.08810.65.93536339.2
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)
12.22.2688.50.7412.25.9

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 REPLACEMENTTHROUGHOUT1RXW2.274.4333535175896.240.201650.200110.23134RANDOM53.506
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]
2.78-0.8-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.983
r_dihedral_angle_4_deg16.431
r_dihedral_angle_3_deg12.677
r_dihedral_angle_1_deg5.508
r_long_range_B_refined5.015
r_long_range_B_other5.008
r_scangle_other3.329
r_mcangle_it2.367
r_mcangle_other2.366
r_scbond_it2.036
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.983
r_dihedral_angle_4_deg16.431
r_dihedral_angle_3_deg12.677
r_dihedral_angle_1_deg5.508
r_long_range_B_refined5.015
r_long_range_B_other5.008
r_scangle_other3.329
r_mcangle_it2.367
r_mcangle_other2.366
r_scbond_it2.036
r_scbond_other2.036
r_mcbond_it1.469
r_mcbond_other1.469
r_angle_refined_deg1.194
r_angle_other_deg0.879
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.003
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 Atoms4752
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing