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Yeast 20S proteasome in complex with Ac-PAD-ep
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, PH 6.8, VAPOR
DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.68 α = 90 b = 301.26 β = 113.23 c = 145.94 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 2011-04-11 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 2.9 50 94.1 0.081 15.5 3.2 224982 224982
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 2.9 3 97.6 0.518 3.3
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 2.9 15 213732 11250 94.2 0.19642 0.19534 0.2008 0.21704 0.221 RANDOM 57.122
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] 3.52 -0.77 -5.59 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.352 r_sphericity_free 33.176 r_dihedral_angle_3_deg 14.516 r_dihedral_angle_4_deg 14.191 r_dihedral_angle_1_deg 5.101 r_sphericity_bonded 4.644 r_long_range_B_refined 2.629 r_long_range_B_other 2.607 r_mcangle_it 2.159 r_mcangle_other 2.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.352 r_sphericity_free 33.176 r_dihedral_angle_3_deg 14.516 r_dihedral_angle_4_deg 14.191 r_dihedral_angle_1_deg 5.101 r_sphericity_bonded 4.644 r_long_range_B_refined 2.629 r_long_range_B_other 2.607 r_mcangle_it 2.159 r_mcangle_other 2.159 r_scangle_other 2.047 r_scbond_it 1.748 r_scbond_other 1.748 r_mcbond_it 1.699 r_mcbond_other 1.699 r_rigid_bond_restr 1.397 r_angle_refined_deg 0.883 r_angle_other_deg 0.704 r_chiral_restr 0.051 r_bond_refined_d 0.004 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 49376 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 63
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement