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Crystal structure of MAGE-A11 bound to the PCF11 degron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 The well solution contained 0.2 M Na acetate, 0.1 M Bis Tris propane pH 7.5 and 20% (w/v) PEG 3350. The drop contained a 1:1 volume ratio of well solution to protein (15 mg/ml in 50 mM Tris, pH 7.4, 200 mM NaCl and 5 mM DTT).
Crystal Properties Matthews coefficient Solvent content 2.71 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.493 α = 77.44 b = 78.195 β = 77.34 c = 72.911 γ = 89.59
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2018-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.19 38.79 96.6 0.12 0.952 19.9 2.4 56569 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.25 0.372 0.757
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 4V0P 2.19 38.79 53723 2846 94.8 0.2069 0.2048 0.2104 0.2461 0.2522 RANDOM 36.814
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] 0.1 -0.57 -0.25 -0.35 1.01 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.91 r_dihedral_angle_4_deg 15.601 r_dihedral_angle_3_deg 14.851 r_dihedral_angle_1_deg 6.337 r_angle_refined_deg 1.48 r_angle_other_deg 1.443 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.91 r_dihedral_angle_4_deg 15.601 r_dihedral_angle_3_deg 14.851 r_dihedral_angle_1_deg 6.337 r_angle_refined_deg 1.48 r_angle_other_deg 1.443 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7095 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling