5FBA

S1 nuclease from Aspergillus oryzae in complex with phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AK0 

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
2.0740.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.765α = 90
b = 62.307β = 106.75
c = 48.003γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-05-30MSINGLE 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
11.845.9795.30.07411.73.12092217.6
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)
11.81.84690.3862.22.2

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 REPLACEMENTTHROUGHOUT1AK01.845.9720820107894.860.153040.152020.19864Random selection21.293
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]
-1.45-1.36-0.522.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.358
r_dihedral_angle_4_deg14.398
r_dihedral_angle_3_deg13.868
r_dihedral_angle_1_deg6.159
r_long_range_B_refined4.4
r_long_range_B_other4.213
r_scangle_other2.812
r_mcangle_it1.969
r_mcangle_other1.969
r_scbond_it1.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.358
r_dihedral_angle_4_deg14.398
r_dihedral_angle_3_deg13.868
r_dihedral_angle_1_deg6.159
r_long_range_B_refined4.4
r_long_range_B_other4.213
r_scangle_other2.812
r_mcangle_it1.969
r_mcangle_other1.969
r_scbond_it1.909
r_scbond_other1.908
r_angle_refined_deg1.688
r_mcbond_it1.433
r_mcbond_other1.431
r_angle_other_deg1.066
r_chiral_restr0.109
r_bond_refined_d0.016
r_bond_other_d0.008
r_gen_planes_refined0.008
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 Atoms2042
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building