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Human 20S Proteasome in complex with peptide activator peptide BLM42
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.915 α = 90 b = 203.262 β = 90 c = 316.421 γ = 90
Symmetry Space Group P 21 21 21
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 DECTRIS EIGER X 16M 2018-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.14 107.181 94.5 0.1366 0.1474 0.055 0.995 6.65 7.1 327921
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.14 2.295 62.9 1.4184 1.5254 0.5585 0.635 1.53 7.41 16397
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 (All) 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 2.14 107.123 327919 16354 81.566 0.198 0.1962 0.1961 0.2261 0.226 RANDOM 47.647
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] -0.295 0.477 -0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.254 r_dihedral_angle_6_deg 13.107 r_lrange_it 6.91 r_dihedral_angle_1_deg 6.118 r_dihedral_angle_2_deg 3.52 r_scangle_it 1.371 r_mcangle_it 1.188 r_angle_refined_deg 0.892 r_scbond_it 0.826 r_mcbond_it 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.254 r_dihedral_angle_6_deg 13.107 r_lrange_it 6.91 r_dihedral_angle_1_deg 6.118 r_dihedral_angle_2_deg 3.52 r_scangle_it 1.371 r_mcangle_it 1.188 r_angle_refined_deg 0.892 r_scbond_it 0.826 r_mcbond_it 0.66 r_nbtor_refined 0.296 r_symmetry_nbd_refined 0.196 r_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.131 r_xyhbond_nbd_refined 0.124 r_ncsr_local_group_4 0.082 r_chiral_restr 0.074 r_ncsr_local_group_8 0.066 r_ncsr_local_group_7 0.062 r_ncsr_local_group_9 0.061 r_ncsr_local_group_1 0.055 r_ncsr_local_group_6 0.051 r_ncsr_local_group_2 0.05 r_ncsr_local_group_3 0.05 r_ncsr_local_group_5 0.049 r_metal_ion_refined 0.047 r_ncsr_local_group_10 0.046 r_ncsr_local_group_12 0.043 r_ncsr_local_group_11 0.042 r_ncsr_local_group_13 0.041 r_ncsr_local_group_14 0.02 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47032 Nucleic Acid Atoms Solvent Atoms 3404 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling Coot model building MOLREP phasing