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Yeast 20S proteasome in complex with PR-957 (morpholine)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYP pdb entry 1RYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 100 mM MES, 12% MPD, 20 mM MgAc2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.68 66.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.41 α = 90 b = 300.78 β = 112.75 c = 143.82 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 2011-02-02 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 3.4 30 98.1 0.143 8.2 144376 141633 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1RYP 3.4 15 141632 134550 7082 98.29 0.18086 0.17885 0.21948 0.1808 RANDOM 80.525
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] 3.86 -2.13 -8.88 3.38
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.533 r_dihedral_angle_2_deg 36.691 r_dihedral_angle_4_deg 13.826 r_dihedral_angle_3_deg 13.737 r_sphericity_bonded 10.839 r_dihedral_angle_1_deg 4.268 r_rigid_bond_restr 1.302 r_angle_refined_deg 0.899 r_chiral_restr 0.059 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.533 r_dihedral_angle_2_deg 36.691 r_dihedral_angle_4_deg 13.826 r_dihedral_angle_3_deg 13.737 r_sphericity_bonded 10.839 r_dihedral_angle_1_deg 4.268 r_rigid_bond_restr 1.302 r_angle_refined_deg 0.899 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49538 Nucleic Acid Atoms Solvent Atoms 1322 Heterogen Atoms 252
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing