6NTT
X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with 1,5-Disulfonyl Naphthalene
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1AVU |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | Lyophilized protein dissolved in water to 25 mg/ml. Sitting drop vapor diffusion against reservoirs of 25% PEG 3350 with 0.10 M MES buffer ph 6.5. 3 ul drops composed of equal amounts of protein stock solution and reservoir supplemented with 0.10 M 1,5-Disulfonyl Naphthalene. Crystallization time about 2 weeks. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.23 | 49 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 41.88 | α = 90 |
b = 64.68 | β = 97.52 |
c = 69.08 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 173 | CCD | MAR CCD 130 mm | 2012-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 1.0 | SSRL | BL7-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | CC (Half) | 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 | 2.4 | 32.61 | 99 | 0.122 | 0.124 | 0.136 | 0.99 | 4.7 | 4.7 | 13649 | 83 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.4 | 2.45 | 85 | 0.481 | 0.538 | 2.2 | 4.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | 1AVU | 2.4 | 32.61 | 12813 | 656 | 93.2 | 0.21376 | 0.20924 | 0.30595 | RANDOM | 68.999 |
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] | |
-1.29 | -2.2 | -1.71 | 3.46 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.46 |
r_dihedral_angle_4_deg | 17.478 |
r_dihedral_angle_3_deg | 15.304 |
r_dihedral_angle_1_deg | 8.191 |
r_long_range_B_refined | 6.946 |
r_long_range_B_other | 6.946 |
r_scangle_other | 3.731 |
r_mcangle_it | 3.302 |
r_mcangle_other | 3.302 |
r_scbond_it | 2.284 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2739 |
Nucleic Acid Atoms | |
Solvent Atoms | 225 |
Heterogen Atoms | 90 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data reduction |
CrystalClear | data scaling |
PHASER | phasing |