X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8A6U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M TRIS, 0.5 M LiCl, 28% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.4950.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.97α = 90
b = 78.12β = 101.44
c = 88.13γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-02-16MSINGLE 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
11.553094.90.03913.12.8107827
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)
11.551.6598.20.5092.1

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 REPLACEMENTTHROUGHOUT8A6U1.5515102435539294.960.14810.1460.1865RANDOM26.745
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]
1.090.59-0.45-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.386
r_dihedral_angle_4_deg16.8
r_dihedral_angle_3_deg14.785
r_dihedral_angle_1_deg5.43
r_rigid_bond_restr3.46
r_angle_refined_deg1.785
r_angle_other_deg1.56
r_chiral_restr0.104
r_bond_refined_d0.013
r_gen_planes_refined0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.386
r_dihedral_angle_4_deg16.8
r_dihedral_angle_3_deg14.785
r_dihedral_angle_1_deg5.43
r_rigid_bond_restr3.46
r_angle_refined_deg1.785
r_angle_other_deg1.56
r_chiral_restr0.104
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5314
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing