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 |