8S2U
SSX structure of Lysozyme grown in batch conditions
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 3 | 294 | Protein dissolved in 20 mM sodium acetate pH 4.6 Protein and precipitant mixed in a 1:4 ratio Precipitant solution: 6% PEG 6000 (w/v), 3.4M NaCl and 1M sodium acetate pH 3.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.06 | 40.38 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 79 | α = 90 |
b = 79 | β = 90 |
c = 37.9 | γ = 90 |
Symmetry | |
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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 | 293 | PIXEL | PSI JUNGFRAU 4M | 2023-01-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.07 | ESRF | ID29 |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | SOS Chip | fixed target |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 29954 | 34032 | 81800 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 79 | 100 | 0.99 | 13.5 | 438 | 11636 | 30.46 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.8 | 1.83 | 100 | 0.49 | 0.2 | 47.67 |
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 | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.8 | 55.924 | 11597 | 581 | 99.991 | 0.173 | 0.1706 | 0.2307 | 38.199 |
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] | |
-0.004 | -0.004 | 0.008 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 13.297 |
r_dihedral_angle_3_deg | 12.871 |
r_dihedral_angle_2_deg | 8.961 |
r_lrange_it | 8.004 |
r_lrange_other | 7.97 |
r_dihedral_angle_1_deg | 6.997 |
r_scangle_it | 6.642 |
r_scangle_other | 6.638 |
r_scbond_it | 4.325 |
r_scbond_other | 4.321 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 59 |
Heterogen Atoms | 2 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
MOLREP | phasing |