3OFW
Crystal structure of recombinant Kunitz Type serine protease Inhibitor-1 from the Carribean sea anemone stichodactyla helianthus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SHP | PDB entry 1SHP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 288.15 | 1.7 M ammonium sulphate, 0.1 M Tris-HCl, 6% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 58.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.158 | α = 90 |
b = 37.158 | β = 90 |
c = 114.98 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | 288 | IMAGE PLATE | MARRESEARCH | 2010-05-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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) | 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 | 2.5 | 35.358 | 3127 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.5 | 2.64 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1SHP | 2.5 | 35.35 | 2 | 3127 | 2955 | 135 | 98.41 | 0.19118 | 0.18972 | 0.22103 | RANDOM | 21.497 |
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] | |
1.06 | 1.06 | -2.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.518 |
r_dihedral_angle_3_deg | 20.866 |
r_dihedral_angle_4_deg | 17.746 |
r_dihedral_angle_1_deg | 7.19 |
r_scangle_it | 3.478 |
r_scbond_it | 2.03 |
r_mcangle_it | 1.533 |
r_angle_refined_deg | 1.402 |
r_mcbond_it | 0.904 |
r_symmetry_hbond_refined | 0.354 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 435 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALA | data scaling |