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Structure of human Mcl-1 in complex with thienopyrimidine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 284 25% PEG3350, 0.2M MAGNESIUM FORMATE, 1MM MALTOSE
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.48 α = 90 b = 135.75 β = 90 c = 38.01 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 2017-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.76 34.39 99.4 0.052 0.06 0.028 0.998 12.9 4 52298
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.81 99.2 0.794 0.504 0.439 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5LOF 1.8 20 46429 2408 99.15 0.1787 0.1771 0.208 0.2219 RANDOM 37.982
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] -0.36 -1.45 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.403 r_dihedral_angle_4_deg 19.013 r_dihedral_angle_3_deg 15.636 r_dihedral_angle_1_deg 5.651 r_angle_refined_deg 1.882 r_angle_other_deg 1.109 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.403 r_dihedral_angle_4_deg 19.013 r_dihedral_angle_3_deg 15.636 r_dihedral_angle_1_deg 5.651 r_angle_refined_deg 1.882 r_angle_other_deg 1.109 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3953 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 48
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing