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Crystal structure of yeast 20S proteasome in complex with vinylketone carmaphycin analogue VNK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 297 30 mM of magnesium acetate, 100 mM of MES (pH 7.2) and 12% of MPD, vapor diffusion, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.87 68.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.85 α = 90 b = 301.36 β = 112.82 c = 144.46 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 2012-06-02 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 2.8 48.42 98.2 0.096 8.76 257429 -3 56.903
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 2.8 2.9 97.8 0.485 2.56
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 48.42 257418 12815 98.31 0.2048 0.2031 0.2032 0.2389 0.2373 RANDOM 65.0692
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] 2.94 -1.91 -7.77 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.877 r_dihedral_angle_3_deg 15.433 r_dihedral_angle_4_deg 14.034 r_dihedral_angle_1_deg 4.912 r_angle_refined_deg 0.95 r_scangle_it 0.795 r_scbond_it 0.435 r_mcangle_it 0.315 r_mcbond_it 0.162 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.877 r_dihedral_angle_3_deg 15.433 r_dihedral_angle_4_deg 14.034 r_dihedral_angle_1_deg 4.912 r_angle_refined_deg 0.95 r_scangle_it 0.795 r_scbond_it 0.435 r_mcangle_it 0.315 r_mcbond_it 0.162 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49538 Nucleic Acid Atoms Solvent Atoms 750 Heterogen Atoms 216
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction CNS phasing