8CZK
Human LanCL1 bound to GSH and Dhb-Erk peptide
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3E6U | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 282 | 0.70-0.75 M succinic acid pH 7.0, 0.1 M bis-tris-propane pH 7.0 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.63 | 53.26 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 55.688 | α = 90 |
| b = 120.562 | β = 90 |
| c = 144.224 | 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 | CCD | RAYONIX MX-300 | 2021-02-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97856 | APS | 21-ID-F |
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 | 1.91 | 92.5 | 100 | 0.119 | 0.126 | 0.041 | 0.998 | 13.5 | 10 | 75709 | |||||||||
| 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) | ||||||||
| 1 | 1.914 | 1.92 | 100 | 1.284 | 1.36 | 0.438 | 0.785 | 2.1 | 10.1 | ||||||||||
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 | 3E6U | 1.91 | 25 | 71871 | 3759 | 99.85 | 0.18542 | 0.184 | 0.21338 | RANDOM | 31.31 | ||||||
| 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] | |
| 0.53 | 2.87 | -3.4 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.254 |
| r_dihedral_angle_4_deg | 15.782 |
| r_dihedral_angle_3_deg | 14.257 |
| r_dihedral_angle_1_deg | 6.297 |
| r_long_range_B_refined | 5.48 |
| r_mcangle_it | 2.185 |
| r_scbond_it | 2.115 |
| r_mcbond_it | 1.416 |
| r_angle_refined_deg | 1.079 |
| r_chiral_restr | 0.094 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6452 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 477 |
| Heterogen Atoms | 96 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| AutoProcess | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
