X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M TRIS, 0.2 M MgCl2, 20% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.5451.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.16α = 90
b = 78.33β = 101.71
c = 89.61γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.6530980.03516.43.194381
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)
11.651.750.4882.4

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 REPLACEMENTTHROUGHOUT1UBX1.651589539471297.860.15730.15530.1946RANDOM36.621
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]
4.333.05-4.71-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.146
r_dihedral_angle_3_deg14.373
r_dihedral_angle_4_deg12.442
r_rigid_bond_restr7.58
r_dihedral_angle_1_deg5.139
r_angle_other_deg1.261
r_angle_refined_deg1.214
r_chiral_restr0.065
r_bond_refined_d0.005
r_gen_planes_refined0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.146
r_dihedral_angle_3_deg14.373
r_dihedral_angle_4_deg12.442
r_rigid_bond_restr7.58
r_dihedral_angle_1_deg5.139
r_angle_other_deg1.261
r_angle_refined_deg1.214
r_chiral_restr0.065
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5190
Nucleic Acid Atoms
Solvent Atoms594
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing