1Y3G
Crystal Structure of a Silanediol Protease Inhibitor Bound to Thermolysin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6 | 294 | MES, DMSO, Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 6.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.2 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 93.52 | ¦Á = 90 |
b = 93.52 | ¦Â = 90 |
c = 131.77 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 298 | IMAGE PLATE | RIGAKU RAXIS IV | 2003-08-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.1 | 31 | 96.1 | 0.111 | 6.4 | 6 | 19569 |
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) | |||||||||||
2.1 | 2.15 | 93.1 | 0.34 | 2.2 | 6.2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | 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 | MOLECULAR REPLACEMENT | 2.1 | 31 | 19568 | 19568 | 1015 | 96.1 | 0.158 | 0.158 | 0.155 | 0.225 | RANDOM |
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] | |
-1.41 | -1.41 | -1.41 | 2.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_dihedral_angle_d | 16.698 |
t_it | 4.865 |
t_angle_deg | 1.057 |
t_gen_planes | 0.014 |
t_bond_d | 0.008 |
t_trig_c_planes | 0.005 |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_nbd |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2432 |
Nucleic Acid Atoms | |
Solvent Atoms | 127 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
TNT | refinement |
PDB_EXTRACT | data extraction |
CCP4 | data scaling |
TNT | phasing |