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Yeast 20S proteasome in complex with the alkaloid indolo-phakellin (4)
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 6.8 297 20 MM MGAC2, 13% MPD, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.08 α = 90 b = 300.88 β = 113.11 c = 145.99 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 2012-09-22 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 30 96.5 0.064 11.9 3.2 379536 366252 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 2.5 2.6 98.7 0.524 2.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RYP 2.5 15 366252 347939 18313 98.77 0.19074 0.18959 0.1958 0.21289 0.217 RANDOM 61.517
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] 2.95 -0.58 -5.34 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.346 r_sphericity_free 26.476 r_sphericity_bonded 15.999 r_dihedral_angle_3_deg 14.432 r_dihedral_angle_4_deg 14.156 r_dihedral_angle_1_deg 5.131 r_long_range_B_refined 3.158 r_long_range_B_other 3.114 r_mcangle_it 2.585 r_mcangle_other 2.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.346 r_sphericity_free 26.476 r_sphericity_bonded 15.999 r_dihedral_angle_3_deg 14.432 r_dihedral_angle_4_deg 14.156 r_dihedral_angle_1_deg 5.131 r_long_range_B_refined 3.158 r_long_range_B_other 3.114 r_mcangle_it 2.585 r_mcangle_other 2.584 r_scangle_other 2.455 r_scbond_it 2.025 r_scbond_other 2.023 r_mcbond_it 1.974 r_mcbond_other 1.974 r_rigid_bond_restr 0.902 r_angle_refined_deg 0.857 r_angle_other_deg 0.691 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49366 Nucleic Acid Atoms Solvent Atoms 970 Heterogen Atoms 53
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing