3GT4
Structure of proteinase K with the magic triangle I3C
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 293 | 0.1M TRIS, 1.28M ammonium sulfate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.784 | α = 90 |
b = 67.784 | β = 90 |
c = 101.845 | 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 | 106 | CCD | MARMOSAIC 225 mm CCD | double crystal Si(111) fixed-exit monochromator | 2008-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.54178 | SLS | X10SA |
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 | 1.76 | 47.9 | 93.8 | 0.048 | 33.8 | 10.14 | 22828 | 22828 |
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 | 1.76 | 1.86 | 62 | 0.13 | 8.3 | 1.73 |
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 | SAD | FREE R | none | 1.76 | 47.9 | 22770 | 22770 | 1137 | 93.8 | 0.141 | 0.14 | 0.14 | 0.191 | RANDOM | 10.204 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.463 |
s_similar_adp_cmpnt | 0.044 |
s_non_zero_chiral_vol | 0.04 |
s_zero_chiral_vol | 0.038 |
s_angle_d | 0.023 |
s_anti_bump_dis_restr | 0.012 |
s_bond_d | 0.007 |
s_similar_dist | 0.006 |
s_approx_iso_adps | |
s_rigid_bond_adp_cmpnt |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1987 |
Nucleic Acid Atoms | |
Solvent Atoms | 343 |
Heterogen Atoms | 53 |
Software
Software | |
---|---|
Software Name | Purpose |
SHELX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SADABS | data scaling |
SHELXD | phasing |
SHELXL-97 | refinement |