5FBD

S1 nuclease from Aspergillus oryzae in complex with phosphate and 2'-deoxycytidine


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 DROP3.82910.1 M Citric acid pH 3.8, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
1.9536.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.04α = 90
b = 62.426β = 90
c = 84.118γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDAGILENT ATLAS CCD2013-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA1.54056

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
11.7530.0895.20.06113.63.7222215.1
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)
11.751.7872.20.3762.12.2

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 S11.7530.0822191113894.270.152880.15150.21159Random selection11.744
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]
0.56-0.840.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.507
r_dihedral_angle_3_deg13.175
r_dihedral_angle_4_deg12.895
r_dihedral_angle_1_deg5.69
r_long_range_B_refined4.753
r_long_range_B_other4.298
r_scangle_other1.99
r_angle_refined_deg1.706
r_mcangle_other1.363
r_mcangle_it1.361
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.507
r_dihedral_angle_3_deg13.175
r_dihedral_angle_4_deg12.895
r_dihedral_angle_1_deg5.69
r_long_range_B_refined4.753
r_long_range_B_other4.298
r_scangle_other1.99
r_angle_refined_deg1.706
r_mcangle_other1.363
r_mcangle_it1.361
r_scbond_it1.318
r_scbond_other1.317
r_angle_other_deg1.1
r_mcbond_it0.88
r_mcbond_other0.873
r_chiral_restr0.119
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
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 Atoms2049
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building