1C2M
RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.98 | TRYPSIN-BENZAMIDINE, P3(1) 2 1 WERE GROWN BY VAPOR DIFFUSION, AS DESCRIBED FOR P2(1) 2(1) 2(1) (LARGE CELL) (MANGEL, ET AL., BIOCHEMISTRY 29, 8351-8357, 1990) THE CRYSTAL WAS SOAKED FOR 25 DAYS IN 2.11 M ZN+2, 250 MM CL-, PH 4.86 IN THE ABSENCE OF AN INHIBITOR. THIS SOLUTION WAS REPLACED ONCE EVERY DAY OR TWO TO REMOVE BOUND BENZAMIDINE AND TO INCORPORATE ZN+2 AT THE ACTIVE SITE. IT WAS THEN SOAKED IN CHLORIDE-FREE SOLUTION OF 1.02 MGSO4 . 7H2O, 1.62 M ZNSO4 . 7 H2O, 0.50 M ZINC ACETATE DIHYDRATE, PH 4.98 FOR 10 DAYS DURING WHICH THE SOAKING SOLUTION WAS REPLACED ONCE A DAY. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.85 | α = 90 |
b = 54.85 | β = 90 |
c = 109.23 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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++ | MSC MIRRORS | 1998-04-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE |
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 | 1.33 | 35.84 | 74 | 0.085 | 8.2 | 2.3 | 32374 | 0.5 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1.4 | 1.46 | 37.4 | 0.345 | 1.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | DIFFERENCE FOURIER PLUS REFINEMENT | X-PLOR | 1.4 | 7.5 | 1.7 | 28118 | 2864 | 74 | 0.195 | 0.195 | 0.234 |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 26.2 |
x_angle_deg | 3.7 |
x_improper_angle_d | 0.52 |
x_bond_d | 0.018 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3297 |
Nucleic Acid Atoms | |
Solvent Atoms | 639 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
bioteX | data collection |
bioteX | data reduction |
X-PLOR | model building |
Quanta | model building |
Insight II | model building |
X-PLOR | refinement |
bioteX | data scaling |
X-PLOR | phasing |