3B72
Crystal structure of lysozyme folded in SDS and 2-methyl-2,4-pentanediol
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 300 | 50mM Tris pH8, 70% MPD and 6mM SDS, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.8 | 29.76 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 77.9 | α = 90 |
| b = 77.9 | β = 90 |
| c = 37.53 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 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 | 100 | CCD | Ruby CCD detector | 2006-10-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SEALED TUBE | OXFORD DIFFRACTION ENHANCE ULTRA | 1.54 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.5 | 10 | 99.7 | 0.123 | 13.7 | 8.2 | 19000 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1.5 | 1.5 | 99.9 | 0.308 | 1.4 | |||||||||||||||
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R | 1Z55 | 1.5 | 10 | 18023 | 912 | 95.1 | 0.2044 | 0.2044 | 0.2407 | RANDOM | 18.23 | ||||||
| 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] | |
| Coordinate Error | ||
|---|---|---|
| Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
| 1136.5 | ||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_similar_adp_cmpnt | 0.071 |
| s_non_zero_chiral_vol | 0.049 |
| s_zero_chiral_vol | 0.046 |
| s_from_restr_planes | 0.0265 |
| s_angle_d | 0.026 |
| s_anti_bump_dis_restr | 0.01 |
| s_bond_d | 0.009 |
| s_similar_dist | |
| s_rigid_bond_adp_cmpnt | |
| s_approx_iso_adps | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1001 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 134 |
| Heterogen Atoms | 3 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELX | model building |
| SHELXL-97 | refinement |
| PHASER | phasing |
