5FBF

S1 nuclease from Aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.82910.1 M Citric acid pH 3.8, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
1.8132.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.742α = 90
b = 62.388β = 90
c = 62.762γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91842BESSY14.1

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
11.0444.2594.50.08910.76962344.8
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)
11.041.0654.50.3072.72.3

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 S11.0444.2596142471294.460.113150.111060.13509Random selection8.324
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]
-0.540.320.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.967
r_sphericity_free21.937
r_dihedral_angle_4_deg11.661
r_dihedral_angle_3_deg11.187
r_rigid_bond_restr8.247
r_dihedral_angle_1_deg5.948
r_sphericity_bonded5.778
r_long_range_B_refined2.764
r_angle_other_deg2.067
r_long_range_B_other1.992
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.967
r_sphericity_free21.937
r_dihedral_angle_4_deg11.661
r_dihedral_angle_3_deg11.187
r_rigid_bond_restr8.247
r_dihedral_angle_1_deg5.948
r_sphericity_bonded5.778
r_long_range_B_refined2.764
r_angle_other_deg2.067
r_long_range_B_other1.992
r_angle_refined_deg1.695
r_scangle_other1.238
r_scbond_other0.933
r_scbond_it0.932
r_mcangle_it0.831
r_mcangle_other0.83
r_mcbond_it0.612
r_mcbond_other0.602
r_chiral_restr0.107
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.009
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building