X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293100mM Tris-HCl (pH 8.5), 1260mM Ammonium sulfate, 200mM Lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.3347.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.318α = 99.17
b = 43.981β = 93.9
c = 130.116γ = 92.87
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
1243.3797.20.0860.1090.9966.292.5964452024.745
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.06950.3420.4290.9272.32.665

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 REPLACEMENTTHROUGHOUT3ELL243.3742292222797.20.23070.22920.2604RANDOM17.047
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]
-0.18-0.57-0.091.49-1.63-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.693
r_dihedral_angle_4_deg21.853
r_dihedral_angle_3_deg12.996
r_dihedral_angle_1_deg6.31
r_angle_other_deg1.663
r_angle_refined_deg1.573
r_chiral_restr0.069
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.693
r_dihedral_angle_4_deg21.853
r_dihedral_angle_3_deg12.996
r_dihedral_angle_1_deg6.31
r_angle_other_deg1.663
r_angle_refined_deg1.573
r_chiral_restr0.069
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5304
Nucleic Acid Atoms
Solvent Atoms624
Heterogen Atoms214

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing