2VI1
Atomic resolution (1.04 A) structure of purified thaumatin I grown in sodium D-tartrate at 22 C.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 7.1 | 295 | MICROBATCH METHOD; PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM D-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 22 C |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.8 | 29.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.939 | α = 90 |
b = 54.304 | β = 90 |
c = 70.808 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC CCD | TOROIDAL FOCUSING MIRROR | 2007-08-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | NSLS | X6A |
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 | 1.04 | 20 | 99 | 0.05 | 36.1 | 7.2 | 93952 | 2 |
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 | 1.04 | 1.06 | 97.7 | 0.7 | 2.2 | 6 |
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 | PDB ENTRY 1KWN | 1.04 | 16.72 | 89156 | 4704 | 100 | 0.129 | 0.128 | 0.14 | RANDOM | 13.11 |
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] | |
0.15 | -0.01 | -0.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.544 |
r_dihedral_angle_4_deg | 18.23 |
r_dihedral_angle_3_deg | 10.963 |
r_dihedral_angle_1_deg | 6.409 |
r_scangle_it | 3.899 |
r_scbond_it | 2.926 |
r_mcangle_it | 2.382 |
r_mcbond_it | 1.665 |
r_angle_refined_deg | 1.56 |
r_nbtor_refined | 0.312 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1551 |
Nucleic Acid Atoms | |
Solvent Atoms | 308 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |