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Yeast 20S proteasome beta2-H114D mutant in complex with Ac-PAE-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, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.71 α = 90 b = 301.32 β = 113.18 c = 145.93 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 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 2.5 50 95.8 0.07 14.1 3.1 339556 339556
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 2.5 2.6 94.1 0.557
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 2.5 15 339556 17872 95.91 0.22687 0.22608 0.2319 0.24174 0.248 RANDOM 53.604
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] 2.26 0.01 -4.64 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.659 r_sphericity_free 30.195 r_dihedral_angle_3_deg 14.742 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_1_deg 5.16 r_sphericity_bonded 4.467 r_long_range_B_refined 2.512 r_long_range_B_other 2.44 r_mcangle_it 1.912 r_mcangle_other 1.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.659 r_sphericity_free 30.195 r_dihedral_angle_3_deg 14.742 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_1_deg 5.16 r_sphericity_bonded 4.467 r_long_range_B_refined 2.512 r_long_range_B_other 2.44 r_mcangle_it 1.912 r_mcangle_other 1.912 r_scangle_other 1.79 r_scbond_it 1.596 r_scbond_other 1.596 r_mcbond_it 1.528 r_mcbond_other 1.528 r_rigid_bond_restr 1.002 r_angle_refined_deg 0.906 r_angle_other_deg 0.734 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 49372 Nucleic Acid Atoms Solvent Atoms 963 Heterogen Atoms 64
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement