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Crystal structure of MCL-1 in complex with a neutralizing Alphabody CMPX-383B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 287 2% (w/v) PEG 3000
0.1 M sodium acetate pH 5.5
0.2 M zinc acetate dihydrate
Crystal Properties Matthews coefficient Solvent content 2.75 58.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.699 α = 90 b = 69.699 β = 90 c = 261.289 γ = 120
Symmetry Space Group P 61 2 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 PILATUS 2M 2016-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87290 ESRF ID23-2
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 2.3 44.33 99.68 0.1112 0.1181 0.03928 1 14.61 8.9 17660 55.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.301 2.383 97.31 0.398 0.85 8.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3MK8 2.3 44.33 17660 1060 99.8 0.2412 0.24 0.254 0.2592 0.2764 RANDOM 80.46
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] -4.5365 -4.5365 9.0731
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.16 t_omega_torsion 2.29 t_angle_deg 0.8 t_bond_d 0.006 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2151 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 5
Software Software Software Name Purpose BUSTER refinement MxCuBE data collection PHASER phasing Coot model building PHENIX model building XDS data scaling XDS data reduction