X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YWK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3293.1530% PEG 4000, 0.2 M sodium acetate, 0.1 M tris, pH 8.3
Crystal Properties
Matthews coefficientSolvent content
2.0740.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.238α = 90
b = 30.476β = 119.87
c = 111.685γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00003SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.1548.4399.10.090.110.0470.99810.75.325440
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2399.20.7550.9120.3930.6771.95.2

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 REPLACEMENTTHROUGHOUT6YWK2.1548.4324153128698.810.18250.18030.2258RANDOM48.745
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]
1.23-0.21-1.590.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.819
r_dihedral_angle_4_deg15.149
r_dihedral_angle_3_deg14.352
r_dihedral_angle_1_deg7.618
r_angle_refined_deg1.372
r_angle_other_deg1.308
r_chiral_restr0.063
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.819
r_dihedral_angle_4_deg15.149
r_dihedral_angle_3_deg14.352
r_dihedral_angle_1_deg7.618
r_angle_refined_deg1.372
r_angle_other_deg1.308
r_chiral_restr0.063
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3838
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing