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Crystal structure of human Mcl-1 in complex with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.94 M Ammonium Citrate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.85 56.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.528 α = 90 b = 90.804 β = 90 c = 94.104 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2016-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96600 ESRF MASSIF-1
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 2.106 28.217 97.3 0.098 0.116 0.06 0.993 5.1 3 37579
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.106 2.182 99.3 0.824 0.984 0.521 0.577 1.8 3.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.106 28.217 37110 1888 96.04 0.21 0.208 0.2496 0.2952 46.24
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] -3.06 3.586 -0.525
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.342 r_dihedral_angle_3_deg 12.911 r_lrange_it 6.545 r_lrange_other 6.507 r_dihedral_angle_1_deg 5.811 r_dihedral_angle_2_deg 4.614 r_scangle_it 4.068 r_scangle_other 4.068 r_mcangle_it 3.332 r_mcangle_other 3.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.342 r_dihedral_angle_3_deg 12.911 r_lrange_it 6.545 r_lrange_other 6.507 r_dihedral_angle_1_deg 5.811 r_dihedral_angle_2_deg 4.614 r_scangle_it 4.068 r_scangle_other 4.068 r_mcangle_it 3.332 r_mcangle_other 3.327 r_scbond_it 2.342 r_scbond_other 2.341 r_mcbond_it 2.017 r_mcbond_other 2.011 r_angle_refined_deg 0.897 r_angle_other_deg 0.314 r_symmetry_xyhbond_nbd_refined 0.209 r_nbd_refined 0.196 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.148 r_symmetry_nbd_refined 0.139 r_nbd_other 0.135 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.045 r_symmetry_xyhbond_nbd_other 0.022 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4043 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing