5KVX
T. danielli thaumatin at 100K, Data set 2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RQW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.3 | 291 | CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (0.9 M SODIUM/POTASSIUM TARTRATE, 0.2 M AMMONIUM SULFATE, 15% GLYCEROL, 25% PEG 8000, 100 MM HEPES PH 7.3) AND PROTEIN (35 MG/ML) IN THE SITTING DROP FORMAT. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.57 | α = 90 |
b = 57.57 | β = 90 |
c = 151.094 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | 100 | CCD | MARMOSAIC 325 mm CCD | 2014-06-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | 1.21549 | SSRL | BL14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.591 | 31.66 | 99 | 0.045 | 0.052 | 0.025 | 14.7 | 4.1 | 34739 | 34739 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.59 | 1.68 | 94.8 | 1.026 | 1.026 | 1.217 | 0.638 | 0.8 | 3.4 | 4754 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1RQW | 1.59 | 31.66 | 32906 | 1733 | 98.7 | 0.1668 | 0.1656 | 0.1907 | RANDOM | 28.549 |
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] | |
0.91 | 0.91 | -1.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.35 |
r_dihedral_angle_4_deg | 18.54 |
r_dihedral_angle_3_deg | 13.795 |
r_dihedral_angle_1_deg | 9.607 |
r_mcangle_it | 3.605 |
r_mcbond_it | 2.627 |
r_mcbond_other | 2.499 |
r_angle_refined_deg | 2.08 |
r_angle_other_deg | 1.138 |
r_chiral_restr | 0.126 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1551 |
Nucleic Acid Atoms | |
Solvent Atoms | 142 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PDB_EXTRACT | data extraction |