3NSJ
The X-ray crystal structure of lymphocyte perforin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 295 | 0.5 M sodium acetate, 0.1 M imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.01 | 75.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.64 | α = 90 |
b = 109.8 | β = 90 |
c = 141.03 | γ = 90 |
Symmetry | |
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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 | ADSC QUANTUM 315r | Silicon mirrors (adaptive and U-bent) | 2010-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.953689 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.75 | 86.636 | 100 | 0.11 | 0.11 | 18.8 | 16.5 | 32550 | 32550 | 85.48 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.75 | 2.9 | 100 | 0.1093 | 0.1093 | 3.1 | 16.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MIRAS | THROUGHOUT | 2.75 | 47.36 | 32550 | 32390 | 1683 | 100 | 0.1971 | 0.1962 | 0.2146 | RANDOM | 80.51 |
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] | |
13.2715 | -12.4774 | -0.7942 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 17.36 |
t_omega_torsion | 2.28 |
t_angle_deg | 0.98 |
t_bond_d | 0.007 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4036 |
Nucleic Acid Atoms | |
Solvent Atoms | 279 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
SCALA | data processing |
SHARP | phasing |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XDS | data reduction |
SCALA | data scaling |
BUSTER | refinement |