9PQ5 | pdb_00009pq5

MBP-Mcl1 in complex with ligand 8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherpreviously solved structure of MBP-Mcl-1 fusion protein was used as a search model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.528519% (w/v) PEG3350, 0.17M Magnesium formate
Crystal Properties
Matthews coefficientSolvent content
2.2445.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.139α = 90
b = 137.018β = 90
c = 38.524γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9999SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.2880.3499.50.032119.965135419
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.281.5399.60.5225

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.2880.34128507691299.550.153080.150920.16050.194560.1989RANDOM24.742
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]
0.15-0.40.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.266
r_sphericity_free21.337
r_dihedral_angle_4_deg16.979
r_dihedral_angle_3_deg12.48
r_rigid_bond_restr9.432
r_sphericity_bonded8.234
r_dihedral_angle_1_deg5.601
r_scbond_it4.143
r_scbond_other4.143
r_scangle_other3.933
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.266
r_sphericity_free21.337
r_dihedral_angle_4_deg16.979
r_dihedral_angle_3_deg12.48
r_rigid_bond_restr9.432
r_sphericity_bonded8.234
r_dihedral_angle_1_deg5.601
r_scbond_it4.143
r_scbond_other4.143
r_scangle_other3.933
r_long_range_B_refined3.922
r_long_range_B_other3.921
r_mcangle_other3.1
r_mcangle_it3.071
r_mcbond_it2.83
r_mcbond_other2.751
r_angle_refined_deg1.826
r_angle_other_deg1.461
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4042
Nucleic Acid Atoms
Solvent Atoms690
Heterogen Atoms69

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
REFMACphasing
PDB_EXTRACTdata extraction