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MBP-Mcl1 in complex with ligand 12
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 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.573 α = 90 b = 137.15 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 2020-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.53 80.58 100 0.083 0.083 0.085 0.996 11.9 8.2 80684
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.556 100 1.487 1.487 1.3 8.5
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 1.53 80.58 76456 4227 99.97 0.17397 0.17192 0.1835 0.21135 0.2248 RANDOM 27.905
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] 0.27 -0.98 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.571 r_dihedral_angle_4_deg 16.214 r_dihedral_angle_3_deg 12.656 r_long_range_B_refined 7.904 r_long_range_B_other 7.829 r_scangle_other 7.27 r_dihedral_angle_1_deg 5.464 r_scbond_it 5.366 r_scbond_other 5.362 r_mcangle_other 3.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.571 r_dihedral_angle_4_deg 16.214 r_dihedral_angle_3_deg 12.656 r_long_range_B_refined 7.904 r_long_range_B_other 7.829 r_scangle_other 7.27 r_dihedral_angle_1_deg 5.464 r_scbond_it 5.366 r_scbond_other 5.362 r_mcangle_other 3.951 r_mcangle_it 3.948 r_mcbond_it 3.2 r_mcbond_other 3.2 r_angle_refined_deg 1.593 r_angle_other_deg 1.263 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4021 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 89
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement XDS data scaling PHASER phasing PDB_EXTRACT data extraction