8IZK
Crystal structure of trypsin-guanidine complex at 2.05 Angstroms resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1CE5 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 291 | 0.1-0.4 M Li2SO4, 16% PEG-3350 and 0.1 M HEPES at pH of 7.8 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.24 | 45.08 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 54.394 | α = 90 |
| b = 58.042 | β = 90 |
| c = 66.189 | 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 | Bruker PHOTON II | 2022-09-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SEALED TUBE | BRUKER D8 QUEST | 1.5406 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 18.57 | 99.9 | 0.197 | 0.98 | 12.8 | 6.9 | 14694 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2 | 2.05 | 0.703 | 0.82 | 3.6 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1CE5 | 2 | 18.58 | 13859 | 793 | 99.8 | 0.17126 | 0.16834 | 0.22517 | RANDOM | 9.323 | ||||||
| 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] | |
| -0.03 | 0.21 | -0.17 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.193 |
| r_dihedral_angle_4_deg | 18.126 |
| r_dihedral_angle_3_deg | 15.586 |
| r_dihedral_angle_1_deg | 7.884 |
| r_long_range_B_refined | 3.986 |
| r_long_range_B_other | 3.734 |
| r_scangle_other | 1.905 |
| r_angle_refined_deg | 1.661 |
| r_angle_other_deg | 1.414 |
| r_scbond_it | 1.27 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1629 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 208 |
| Heterogen Atoms | 20 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PROTEUM PLUS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
