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Crystal structure of Mcl-1 in complex with compound 65
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 100 mM Bicine pH 8.5, 35% PEG 1500 and 10% ethanol
Crystal Properties Matthews coefficient Solvent content 1.99 38.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.229 α = 90 b = 48.245 β = 108.5 c = 40.707 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 CCD ADSC QUANTUM 315r 2011-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.61 50 99 0.058 0.991 18.9 3.5 17834
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.67 99 0.53 0.734 2.2 3.2
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 3mk8 1.61 38.6 16917 907 97.16 0.19119 0.18997 0.2004 0.21347 0.2258 RANDOM 23.525
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] -0.03 0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.632 r_dihedral_angle_4_deg 16.78 r_dihedral_angle_3_deg 13.816 r_long_range_B_refined 4.239 r_long_range_B_other 4.145 r_dihedral_angle_1_deg 4.098 r_scangle_other 2.506 r_mcangle_it 1.866 r_mcangle_other 1.865 r_scbond_it 1.512
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.632 r_dihedral_angle_4_deg 16.78 r_dihedral_angle_3_deg 13.816 r_long_range_B_refined 4.239 r_long_range_B_other 4.145 r_dihedral_angle_1_deg 4.098 r_scangle_other 2.506 r_mcangle_it 1.866 r_mcangle_other 1.865 r_scbond_it 1.512 r_scbond_other 1.511 r_angle_refined_deg 1.385 r_mcbond_it 1.144 r_mcbond_other 1.135 r_angle_other_deg 0.907 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 1189 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing