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Crystal structure of the MBP-MCL1 complex with highly selective and potent inhibitor of MCL1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 284 25% PEG3350, 0.2M Magnesium Formate, 1mM Maltose
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.4 α = 90 b = 136.76 β = 90 c = 38.33 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2015-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.17 50 99 0.057 0.999 16.7 4.5 28314 1 46.8
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) Redundancy Number Unique Reflections (All) 1 2.17 2.3 97.5 0.52 0.909 2.2 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WGI 2.2 50 25921 1336 99.31 0.18379 0.18107 0.1907 0.23525 0.2363 RANDOM 47.536
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 -4.52 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.266 r_dihedral_angle_4_deg 21.734 r_dihedral_angle_3_deg 17.812 r_long_range_B_other 8.821 r_long_range_B_refined 8.82 r_scangle_other 6.379 r_dihedral_angle_1_deg 5.721 r_mcangle_it 4.866 r_mcangle_other 4.865 r_scbond_other 4.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.266 r_dihedral_angle_4_deg 21.734 r_dihedral_angle_3_deg 17.812 r_long_range_B_other 8.821 r_long_range_B_refined 8.82 r_scangle_other 6.379 r_dihedral_angle_1_deg 5.721 r_mcangle_it 4.866 r_mcangle_other 4.865 r_scbond_other 4.164 r_scbond_it 4.163 r_mcbond_it 3.508 r_mcbond_other 3.508 r_angle_refined_deg 1.647 r_angle_other_deg 1.009 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 3975 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing