X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RIY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529330% PEG3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 5% 1,3-butandiol
Crystal Properties
Matthews coefficientSolvent content
2.2745.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.326α = 97.39
b = 55.969β = 99.29
c = 123.034γ = 90.52
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2016-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000030SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.3243.7791.50.0590.9996.82227669
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.321.488.10.9590.7231.11.9

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 REPLACEMENTTHROUGHOUT3RIY1.3243.77224952238891.870.160760.160250.20856RANDOM21.373
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]
-2.343.38-2.91-1.760.814.1
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free47.72
r_dihedral_angle_2_deg34.612
r_dihedral_angle_4_deg20.43
r_sphericity_bonded19.296
r_dihedral_angle_3_deg13.724
r_long_range_B_refined9.451
r_long_range_B_other9.451
r_mcangle_it8.762
r_mcangle_other8.762
r_scangle_other7.766
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free47.72
r_dihedral_angle_2_deg34.612
r_dihedral_angle_4_deg20.43
r_sphericity_bonded19.296
r_dihedral_angle_3_deg13.724
r_long_range_B_refined9.451
r_long_range_B_other9.451
r_mcangle_it8.762
r_mcangle_other8.762
r_scangle_other7.766
r_mcbond_it7.279
r_mcbond_other7.278
r_scbond_it7.102
r_scbond_other7.101
r_rigid_bond_restr6.781
r_dihedral_angle_1_deg6.418
r_angle_refined_deg2.886
r_angle_other_deg1.801
r_chiral_restr0.276
r_bond_refined_d0.031
r_gen_planes_refined0.017
r_gen_planes_other0.01
r_bond_other_d0.005
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 Atoms8313
Nucleic Acid Atoms
Solvent Atoms1086
Heterogen Atoms440

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing