3WU8
Spatiotemporal development of soaked protein crystal; derivative 1080 sec
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2LYM | PDB ENTRY 2LYM |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH METHOD | 4.5 | 293 | 25mg/ml Lysozyme, 0.05M SODIUM ACETATE, 0.7M SODIUM CHLORIDE, pH 4.5, BATCH METHOD, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.07 | 40.62 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 79.206 | α = 90 |
b = 79.206 | β = 90 |
c = 37.858 | 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 | 300 | CCD | MARMOSAIC 225 mm CCD | 2013-11-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B2 | 1.07345 | SPring-8 | BL26B2 |
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 | 2 | 50 | 99.6 | 0.082 | 22.8 | 6.9 | 8599 | 8563 | -3 |
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 | 2 | 2.03 | 99.8 | 0.268 | 5.1 | 7 | 404 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 2LYM | 2 | 50 | 8567 | 8541 | 402 | 99.7 | 0.17167 | 0.17167 | 0.16959 | 0.21639 | RANDOM | 19.909 |
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] | |
-0.21 | -0.21 | 0.41 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.285 |
r_dihedral_angle_4_deg | 21.358 |
r_dihedral_angle_3_deg | 16.475 |
r_long_range_B_refined | 7.212 |
r_dihedral_angle_1_deg | 6.202 |
r_scbond_it | 3.114 |
r_mcangle_it | 2.568 |
r_mcbond_it | 1.615 |
r_angle_refined_deg | 1.572 |
r_chiral_restr | 0.118 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms | 4 |
Software
Software | |
---|---|
Software Name | Purpose |
BSS | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |