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MBP-Mcl1 in complex with ligand 21
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 0.11 M Mg Formate, 19.0% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.324 α = 90 b = 137.421 β = 90 c = 38.563 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 2021-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9795 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 1.94 80.5 99.9 0.126 0.135 0.048 0.996 9.3 8 39870
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 1.943 1.977 100 1.749 1.868 0.646 0.552 1.3 8.4
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 1.94 80.5 37786 2044 99.8 0.19754 0.1954 0.1967 0.23753 0.2349 RANDOM 51.252
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] -1.16 -1.94 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.312 r_dihedral_angle_4_deg 15.355 r_dihedral_angle_3_deg 13.07 r_long_range_B_refined 8.096 r_long_range_B_other 8.091 r_dihedral_angle_1_deg 6.111 r_scangle_other 6.086 r_scbond_it 4.666 r_scbond_other 4.665 r_mcangle_it 3.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.312 r_dihedral_angle_4_deg 15.355 r_dihedral_angle_3_deg 13.07 r_long_range_B_refined 8.096 r_long_range_B_other 8.091 r_dihedral_angle_1_deg 6.111 r_scangle_other 6.086 r_scbond_it 4.666 r_scbond_other 4.665 r_mcangle_it 3.957 r_mcangle_other 3.956 r_mcbond_it 3.254 r_mcbond_other 3.254 r_angle_refined_deg 1.521 r_angle_other_deg 1.29 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4043 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction PHASER phasing autoPROC data scaling