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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 279 1.8 M triammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.94 α = 90 b = 39.94 β = 90 c = 326.77 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 2010-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 54.54 96.9 0.104 0.036 14.4 8.2 11265
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 83.8 0.455 0.215 4.1 4.5
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 2.01 20.001 11055 544 96.821 0.207 0.2061 0.2155 0.2223 0.2294 44.298
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] 0.832 0.416 0.832 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.493 r_dihedral_angle_6_deg 13.534 r_lrange_other 12.134 r_lrange_it 12.128 r_scangle_it 8.375 r_scangle_other 8.37 r_dihedral_angle_2_deg 7.171 r_mcangle_it 5.998 r_mcangle_other 5.997 r_scbond_it 5.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.493 r_dihedral_angle_6_deg 13.534 r_lrange_other 12.134 r_lrange_it 12.128 r_scangle_it 8.375 r_scangle_other 8.37 r_dihedral_angle_2_deg 7.171 r_mcangle_it 5.998 r_mcangle_other 5.997 r_scbond_it 5.489 r_scbond_other 5.484 r_dihedral_angle_1_deg 5.288 r_mcbond_it 4.24 r_mcbond_other 4.224 r_angle_refined_deg 1.685 r_angle_other_deg 0.567 r_nbd_refined 0.241 r_symmetry_xyhbond_nbd_refined 0.206 r_nbtor_refined 0.192 r_symmetry_nbd_other 0.19 r_xyhbond_nbd_refined 0.176 r_nbd_other 0.171 r_symmetry_nbd_refined 0.144 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.077 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1182 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing