X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293.1530% broad-molecular-weight PEG smears, 0.1 M MgCl2, 0.1 M tris, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2545.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.617α = 90
b = 111.339β = 90
c = 195.184γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00001SLSX06SA

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
12.0548.899.70.1410.1660.0640.9958.36.253878
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)
12.052.1299.80.8390.9980.3870.6951.96.3

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 REPLACEMENTTHROUGHOUT6ywk2.0548.851148266299.470.17920.17720.2168RANDOM26.716
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]
1.04-0.39-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.092
r_dihedral_angle_4_deg18.864
r_dihedral_angle_3_deg12.823
r_dihedral_angle_1_deg7.396
r_angle_refined_deg1.426
r_angle_other_deg1.363
r_chiral_restr0.072
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.092
r_dihedral_angle_4_deg18.864
r_dihedral_angle_3_deg12.823
r_dihedral_angle_1_deg7.396
r_angle_refined_deg1.426
r_angle_other_deg1.363
r_chiral_restr0.072
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6488
Nucleic Acid Atoms
Solvent Atoms514
Heterogen Atoms175

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing