X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OQ64OQ6,4MBP
experimental modelPDB 4MBP4OQ6,4MBP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729810 MG/ML MBP-MCL1 VCID 9272, 200MM MG FORMATE, 20% PEG3350, 1MM MALTOSE, 2MM ligand 5, CRYOPROTECTANT 20% ETHYLENE GLYCOL, PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2445.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.94α = 90
b = 136.3β = 90
c = 37.8γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2014-09-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.95099.80.0520.05720.99641212-327.19
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.951000.4810.5263.68

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4OQ6,4MBP1.941.2881.3541207189799.770.18180.18020.214530.8327
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.247
f_angle_d0.949
f_chiral_restr0.038
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3862
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms68

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction