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Myeloid cell leukemia-1 (Mcl-1) complexed with compound 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 25-30% PEG 3350, 0.1 M Bis-TRIS pH 6.5, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.31 46.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.613 α = 90 b = 87.678 β = 102.422 c = 50.348 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M 2016-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9785 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.06 28.386 97.79 0.078 0.06 0.983 12.2 2.2 18204
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 2.06 2.1 94 0.357 0.327 0.214 1.9 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.068 28.386 17663 839 87.976 0.193 0.1894 0.189 0.2582 0.2581 31.793
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] 0.414 0.586 -1.409 0.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.363 r_dihedral_angle_3_deg 14.457 r_lrange_it 10.481 r_dihedral_angle_2_deg 7.333 r_dihedral_angle_1_deg 6.671 r_scangle_it 6.439 r_mcangle_it 5.567 r_scbond_it 4.497 r_mcbond_it 3.77 r_angle_refined_deg 1.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.363 r_dihedral_angle_3_deg 14.457 r_lrange_it 10.481 r_dihedral_angle_2_deg 7.333 r_dihedral_angle_1_deg 6.671 r_scangle_it 6.439 r_mcangle_it 5.567 r_scbond_it 4.497 r_mcbond_it 3.77 r_angle_refined_deg 1.832 r_nbtor_refined 0.301 r_symmetry_nbd_refined 0.266 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.177 r_ncsr_local_group_1 0.15 r_chiral_restr 0.12 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2417 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data scaling HKL-2000 data reduction PHASER phasing