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Yeast 20S proteasome at 2.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYP
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 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.02 α = 90 b = 300.93 β = 113.13 c = 145.76 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 PSI PILATUS 6M 2014-10-14 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 2.3 30 98.7 0.061 13.1 3.3 479157 472928
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 2.3 2.4 92.7 0.479 2
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 1RYP 2.3 15 449280 23647 98.84 0.21171 0.21083 0.2138 0.22838 0.2325 RANDOM 55.781
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] 3.02 0.11 -5.17 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.539 r_sphericity_free 28.555 r_dihedral_angle_3_deg 14.72 r_dihedral_angle_4_deg 14.667 r_dihedral_angle_1_deg 5.177 r_sphericity_bonded 3.8 r_long_range_B_refined 2.224 r_long_range_B_other 2.085 r_mcangle_it 1.537 r_mcangle_other 1.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.539 r_sphericity_free 28.555 r_dihedral_angle_3_deg 14.72 r_dihedral_angle_4_deg 14.667 r_dihedral_angle_1_deg 5.177 r_sphericity_bonded 3.8 r_long_range_B_refined 2.224 r_long_range_B_other 2.085 r_mcangle_it 1.537 r_mcangle_other 1.537 r_scangle_other 1.384 r_scbond_it 1.297 r_scbond_other 1.296 r_mcbond_it 1.263 r_mcbond_other 1.263 r_angle_refined_deg 0.888 r_angle_other_deg 0.707 r_rigid_bond_restr 0.552 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 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 49333 Nucleic Acid Atoms Solvent Atoms 1520 Heterogen Atoms 10
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement