5LOF

Crystal structure of the MBP-MCL1 complex with highly selective and potent inhibitor of MCL1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP28425% PEG3350, 0.2M Magnesium Formate, 1mM Maltose
Crystal Properties
Matthews coefficientSolvent content
2.346.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.4α = 90
b = 136.76β = 90
c = 38.33γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.97857SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.1750990.0570.99916.74.528314146.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.172.397.50.520.9092.24.4

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 REPLACEMENTTHROUGHOUT4WGI2.25025921133699.310.183790.181070.23525RANDOM47.536
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]
3.01-4.521.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.266
r_dihedral_angle_4_deg21.734
r_dihedral_angle_3_deg17.812
r_long_range_B_other8.821
r_long_range_B_refined8.82
r_scangle_other6.379
r_dihedral_angle_1_deg5.721
r_mcangle_it4.866
r_mcangle_other4.865
r_scbond_other4.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.266
r_dihedral_angle_4_deg21.734
r_dihedral_angle_3_deg17.812
r_long_range_B_other8.821
r_long_range_B_refined8.82
r_scangle_other6.379
r_dihedral_angle_1_deg5.721
r_mcangle_it4.866
r_mcangle_other4.865
r_scbond_other4.164
r_scbond_it4.163
r_mcbond_it3.508
r_mcbond_other3.508
r_angle_refined_deg1.647
r_angle_other_deg1.009
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3975
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing