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MBP-Mcl1 in complex with ligand 11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 285 0.17 M Mg Formate, 25.00% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.88 α = 90 b = 137.35 β = 90 c = 38.676 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 EIGER2 X 16M 2020-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000021 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.4 80.25 94.5 0.078 0.084 0.029 0.99 13.2 8.2 84015
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.517 1.47 1.56 0.52 0.58 1.5
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 1.4 80.25 79635 4379 80.73 0.14479 0.14204 0.1409 0.19398 0.1926 RANDOM 23.806
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] -0.13 -0.11 0.24
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.042 r_dihedral_angle_2_deg 33.492 r_dihedral_angle_4_deg 18.17 r_dihedral_angle_3_deg 12.387 r_sphericity_bonded 10.123 r_rigid_bond_restr 5.861 r_long_range_B_refined 5.369 r_dihedral_angle_1_deg 5.208 r_long_range_B_other 4.702 r_scangle_other 4.544
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.042 r_dihedral_angle_2_deg 33.492 r_dihedral_angle_4_deg 18.17 r_dihedral_angle_3_deg 12.387 r_sphericity_bonded 10.123 r_rigid_bond_restr 5.861 r_long_range_B_refined 5.369 r_dihedral_angle_1_deg 5.208 r_long_range_B_other 4.702 r_scangle_other 4.544 r_scbond_it 4.313 r_scbond_other 4.301 r_mcangle_it 3.322 r_mcangle_other 3.321 r_mcbond_other 2.852 r_mcbond_it 2.847 r_angle_other_deg 1.62 r_angle_refined_deg 1.277 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 647 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement PHASER phasing autoPROC data reduction autoPROC data scaling