5FBG

S1 nuclease from Aspergillus oryzae, mutant D65N, in complex with phosphate, 2'-deoxycytidine and 2'-deoxyguanosine.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherour previous model of S1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52910.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
3.6466.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.76α = 90
b = 106.76β = 90
c = 127.91γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.9737.4799.60.1319.35.85985210.4
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)
11.972.0297.60.64523.6

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 REPLACEMENTTHROUGHOUTour previous model of S11.9737.4759809302499.630.158890.15790.18705Random selection21.934
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]
0.350.180.35-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.276
r_dihedral_angle_3_deg12.465
r_dihedral_angle_4_deg11.605
r_long_range_B_refined6.252
r_long_range_B_other5.644
r_dihedral_angle_1_deg5.547
r_scangle_other3.656
r_scbond_it2.356
r_scbond_other2.355
r_mcangle_it2.261
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.276
r_dihedral_angle_3_deg12.465
r_dihedral_angle_4_deg11.605
r_long_range_B_refined6.252
r_long_range_B_other5.644
r_dihedral_angle_1_deg5.547
r_scangle_other3.656
r_scbond_it2.356
r_scbond_other2.355
r_mcangle_it2.261
r_mcangle_other2.261
r_angle_refined_deg1.598
r_mcbond_it1.587
r_mcbond_other1.58
r_angle_other_deg1.483
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.009
r_gen_planes_other0.006
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 Atoms4084
Nucleic Acid Atoms
Solvent Atoms652
Heterogen Atoms123

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building