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MBP-Mcl1 in complex with ligand 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other previously solved structure of MBP-Mcl-1 fusion protein was used as a search model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 285 19% (w/v) PEG3350, 0.17M Magnesium formate
Crystal Properties Matthews coefficient Solvent content 2.24 45.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.139 α = 90 b = 137.018 β = 90 c = 38.524 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2019-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.28 80.34 99.5 0.032 1 19.96 5 135419
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.53 99.6 0.522 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 (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 1.28 80.34 128507 6912 99.55 0.15308 0.15092 0.1605 0.19456 0.1989 RANDOM 24.742
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] 0.15 -0.4 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.266 r_sphericity_free 21.337 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_3_deg 12.48 r_rigid_bond_restr 9.432 r_sphericity_bonded 8.234 r_dihedral_angle_1_deg 5.601 r_scbond_it 4.143 r_scbond_other 4.143 r_scangle_other 3.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.266 r_sphericity_free 21.337 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_3_deg 12.48 r_rigid_bond_restr 9.432 r_sphericity_bonded 8.234 r_dihedral_angle_1_deg 5.601 r_scbond_it 4.143 r_scbond_other 4.143 r_scangle_other 3.933 r_long_range_B_refined 3.922 r_long_range_B_other 3.921 r_mcangle_other 3.1 r_mcangle_it 3.071 r_mcbond_it 2.83 r_mcbond_other 2.751 r_angle_refined_deg 1.826 r_angle_other_deg 1.461 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4042 Nucleic Acid Atoms Solvent Atoms 690 Heterogen Atoms 69
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement REFMAC phasing PDB_EXTRACT data extraction