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Yeast 20S proteasome in complex with belactosin C derivative 3
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 = 136.085 α = 90 b = 301.299 β = 113.33 c = 144.582 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 2014-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.0 MPG/DESY, HAMBURG BW6
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 3 50 98 0.118 10.7 3.2 207849 207849 2 2
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 3 3.04 99 0.499 1.9
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 3 15 197382 10427 97.7 0.20536 0.20412 0.2085 0.22907 0.2321 RANDOM 61.7
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] 5.37 -2 -5.98 1.07
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.757 r_dihedral_angle_2_deg 34.272 r_dihedral_angle_3_deg 14.387 r_dihedral_angle_4_deg 14.223 r_sphericity_bonded 5.414 r_dihedral_angle_1_deg 5.187 r_long_range_B_refined 2.918 r_long_range_B_other 2.901 r_mcangle_it 2.501 r_mcangle_other 2.501
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.757 r_dihedral_angle_2_deg 34.272 r_dihedral_angle_3_deg 14.387 r_dihedral_angle_4_deg 14.223 r_sphericity_bonded 5.414 r_dihedral_angle_1_deg 5.187 r_long_range_B_refined 2.918 r_long_range_B_other 2.901 r_mcangle_it 2.501 r_mcangle_other 2.501 r_scangle_other 2.287 r_mcbond_it 1.91 r_mcbond_other 1.91 r_scbond_it 1.901 r_scbond_other 1.9 r_rigid_bond_restr 1.151 r_angle_refined_deg 0.899 r_angle_other_deg 0.695 r_chiral_restr 0.053 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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 276 Heterogen Atoms 150
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC phasing REFMAC refinement XDS data reduction XSCALE data scaling