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Crystal structure of human MBP-Myeloid cell leukemia 1 (Mcl-1) in complex with BRD810 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WGI Same construct
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 3.75 mg/mL MBP-MCL1, 17.5 mM HEPES pH 7.5, 8% PEG 3350, 5% MPD, 5% DMSO, 2.5% PEG400, 75mM NaCl, 25mM Magnesium Formate, 0.75mM DTT, 0.75 mM Maltose, 0.5mM ANJ810, 0.375% glycerol, ~10-4 diluted microseeds, equilibrated against 1.5M NaCl in a EasyXtal 15-Well DropGuard Crystallization Tool
Crystal Properties Matthews coefficient Solvent content 2.25 45.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.301 α = 90 b = 136.957 β = 90 c = 38.257 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 EIGER2 X 16M 2018-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97903 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.56 80 99.71 0.037 0.04 1 20.5 7.1 74575 25.74
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 1.56 1.59 97.3 0.663 0.909 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.56 79.86 1.34 74453 3735 99.59 0.1898 0.1883 0.1883 0.2181 0.2182
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 Key Refinement Restraint Deviation f_dihedral_angle_d 5.476 f_angle_d 0.878 f_chiral_restr 0.053 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4042 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement Aimless data scaling DIALS data reduction PHENIX phasing