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Crystal structure of yeast 20S proteasome in complex with the natural product carmaphycin A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 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 3.83 67.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.62 α = 90 b = 300.28 β = 112.49 c = 144.57 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 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 49.59 98 0.103 7.94 254447 -3 56.13
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 99.1 0.481 2.61
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 49.59 254440 12672 98.1 0.206 0.204 0.2049 0.239 0.237 RANDOM 62.84
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] 3.56 -1.72 -7.79 2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.842 r_dihedral_angle_3_deg 15.486 r_dihedral_angle_4_deg 13.68 r_dihedral_angle_1_deg 4.919 r_angle_refined_deg 0.949 r_scangle_it 0.768 r_scbond_it 0.425 r_mcangle_it 0.291 r_mcbond_it 0.148 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.842 r_dihedral_angle_3_deg 15.486 r_dihedral_angle_4_deg 13.68 r_dihedral_angle_1_deg 4.919 r_angle_refined_deg 0.949 r_scangle_it 0.768 r_scbond_it 0.425 r_mcangle_it 0.291 r_mcbond_it 0.148 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49538 Nucleic Acid Atoms Solvent Atoms 954 Heterogen Atoms 210
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction