X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YLL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.7527731% PEG 400, 0.25 M lithium sulfate and 0.1 M Tris, pH 8.75
Crystal Properties
Matthews coefficientSolvent content
3.2361.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 245.886α = 90
b = 65.889β = 115.5
c = 148.337γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

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
12.949.0498.80.1240.1730.0980.9856.92.94740635.9
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)
12.93.06990.5730.7940.4480.6611.82.9

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 REPLACEMENTTHROUGHOUT4yll2.949.0445144225798.550.20370.20180.2417RANDOM48.558
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]
1.36-0.55-1.380.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.274
r_dihedral_angle_4_deg19.036
r_dihedral_angle_3_deg14.83
r_dihedral_angle_1_deg6.254
r_angle_refined_deg1.203
r_angle_other_deg0.786
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.274
r_dihedral_angle_4_deg19.036
r_dihedral_angle_3_deg14.83
r_dihedral_angle_1_deg6.254
r_angle_refined_deg1.203
r_angle_other_deg0.786
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11385
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms248

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing