4LDT
The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293.15 | 1:1 mix of 12 mg/mL purified complex and well solution (100 mM Bis-Tris, pH 6.0, 200 mM magnesium chloride, 22% PEG3350), crystals appeared in about 2 to 3 days, cryoprotection with well solution + 10% ethylene glycol, flash frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.41 | 48.86 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 104.894 | α = 90 |
| b = 131.612 | β = 90 |
| c = 46.501 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 77 | CCD | MARMOSAIC 300 mm CCD | 2012-03-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1 | APS | 23-ID-D |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.901 | 33.65 | 99 | 0.13 | 8.5 | 8 | 51642 | 51582 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.901 | 1.93 | 95.4 | 0.57 | 1.7 | 3.1 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB ENTRY 4DHZ | 1.901 | 33.65 | 51047 | 48379 | 2612 | 98.82 | 0.19342 | 0.1918 | 0.22318 | RANDOM | 30.507 | |||||
| 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] | |
| 0.36 | -2.07 | 1.71 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.043 |
| r_dihedral_angle_4_deg | 14.683 |
| r_dihedral_angle_3_deg | 13.643 |
| r_dihedral_angle_1_deg | 5.591 |
| r_angle_refined_deg | 1.248 |
| r_angle_other_deg | 0.741 |
| r_chiral_restr | 0.073 |
| r_bond_refined_d | 0.009 |
| r_gen_planes_refined | 0.006 |
| r_bond_other_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4362 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 316 |
| Heterogen Atoms | 17 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| REFMAC | phasing |
