X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M MES, 0.2 M MgCl2, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.5451.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.21α = 90
b = 78.25β = 101.84
c = 89.26γ = 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
11.93098.30.0946.93.461843
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)
11.9299.40.5382.4

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 REPLACEMENTTHROUGHOUT8A6U1.91558621308698.10.20170.19970.2415RANDOM34.126
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]
-2.892.280.251.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.324
r_dihedral_angle_4_deg15.759
r_dihedral_angle_3_deg14.663
r_dihedral_angle_1_deg5.154
r_angle_refined_deg1.173
r_angle_other_deg1.158
r_rigid_bond_restr0.472
r_chiral_restr0.056
r_gen_planes_refined0.003
r_bond_refined_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.324
r_dihedral_angle_4_deg15.759
r_dihedral_angle_3_deg14.663
r_dihedral_angle_1_deg5.154
r_angle_refined_deg1.173
r_angle_other_deg1.158
r_rigid_bond_restr0.472
r_chiral_restr0.056
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5309
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing