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Yeast 20S proteasome double mutant: beta5_F(-46)S / beta5_G128V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CZ4 Yeast 20S proteasome at 2.3 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 20 mM MgAC2, 13% MPD, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 3.61 65.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.72 α = 90 b = 300.35 β = 112.8 c = 144.55 γ = 90
Symmetry Space Group P 1 21 1
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 2016-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 30 97.8 0.064 15.5 3.2 316457
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.7 98.1 0.501 3 3.1
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 2.6 15 299136 15744 97.38 0.18758 0.18563 0.1847 0.22441 0.2232 RANDOM 51.841
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] -1.33 -1.23 4.55 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.397 r_dihedral_angle_4_deg 16.34 r_dihedral_angle_3_deg 15.678 r_long_range_B_refined 6.674 r_long_range_B_other 6.518 r_dihedral_angle_1_deg 6.487 r_rigid_bond_restr 4.73 r_mcangle_it 4.151 r_mcangle_other 4.151 r_scangle_other 4.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.397 r_dihedral_angle_4_deg 16.34 r_dihedral_angle_3_deg 15.678 r_long_range_B_refined 6.674 r_long_range_B_other 6.518 r_dihedral_angle_1_deg 6.487 r_rigid_bond_restr 4.73 r_mcangle_it 4.151 r_mcangle_other 4.151 r_scangle_other 4.105 r_scbond_it 2.926 r_scbond_other 2.926 r_mcbond_it 2.898 r_mcbond_other 2.898 r_angle_refined_deg 1.242 r_angle_other_deg 1.139 r_chiral_restr 0.043 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49473 Nucleic Acid Atoms Solvent Atoms 835 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing