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Yeast 20S proteasome beta2-H114D mutant 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 = 136.77 α = 90 b = 302.73 β = 113.19 c = 145.98 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 2.6 50 96.4 0.074 12 3 321495 321495
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 2.6 2.7 96.2 0.528 2.4
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 2.6 15 305420 16075 96.5 0.21805 0.2173 0.2223 0.23248 0.2363 RANDOM 57.842
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] 2.8 -0.18 -4.74 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.219 r_sphericity_free 33.01 r_dihedral_angle_3_deg 14.227 r_dihedral_angle_4_deg 13.886 r_dihedral_angle_1_deg 5.035 r_sphericity_bonded 4.619 r_long_range_B_refined 2.556 r_long_range_B_other 2.482 r_mcangle_it 2.033 r_mcangle_other 2.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.219 r_sphericity_free 33.01 r_dihedral_angle_3_deg 14.227 r_dihedral_angle_4_deg 13.886 r_dihedral_angle_1_deg 5.035 r_sphericity_bonded 4.619 r_long_range_B_refined 2.556 r_long_range_B_other 2.482 r_mcangle_it 2.033 r_mcangle_other 2.033 r_scangle_other 1.872 r_mcbond_it 1.619 r_mcbond_other 1.619 r_scbond_it 1.619 r_scbond_other 1.618 r_rigid_bond_restr 1.091 r_angle_refined_deg 0.893 r_angle_other_deg 0.736 r_chiral_restr 0.051 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 788 Heterogen Atoms 63
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement