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Structure of Mcl-1 complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 279 0.1 M tri sodium citrate / citric acid buffer pH 4.0, 25% Peg3350
Crystal Properties Matthews coefficient Solvent content 2.1 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.22 α = 90 b = 39.22 β = 90 c = 328.31 γ = 120
Symmetry Space Group P 65 2 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 CCD ADSC QUANTUM 315r 2011-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.77 33.8 94.9 0.037 25.3 8.5 15185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.82 78.8 0.62 2.4 6.3
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 1.9 15 12668 650 97.125 0.196 0.1943 0.2062 0.2393 0.2523 41.271
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] 1.084 0.542 1.084 -3.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.676 r_dihedral_angle_6_deg 14.45 r_lrange_it 10.779 r_lrange_other 10.778 r_scangle_it 8.249 r_scangle_other 8.249 r_dihedral_angle_2_deg 7.804 r_mcangle_it 5.64 r_mcangle_other 5.637 r_scbond_it 5.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.676 r_dihedral_angle_6_deg 14.45 r_lrange_it 10.779 r_lrange_other 10.778 r_scangle_it 8.249 r_scangle_other 8.249 r_dihedral_angle_2_deg 7.804 r_mcangle_it 5.64 r_mcangle_other 5.637 r_scbond_it 5.35 r_scbond_other 5.346 r_dihedral_angle_1_deg 5.048 r_mcbond_it 4.045 r_mcbond_other 4.045 r_angle_refined_deg 1.81 r_angle_other_deg 0.573 r_symmetry_xyhbond_nbd_refined 0.239 r_symmetry_nbd_refined 0.231 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.207 r_nbtor_refined 0.182 r_symmetry_nbd_other 0.181 r_nbd_other 0.163 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1144 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing