6RGX
TETR(D) N82A MUTANT IN COMPLEX WITH DOXYCYCLINE AND MAGNESIUM
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5FKK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 295 | precipitant: 0.1 M HEPES pH 7.5, 1.75M (NH4)2SO4, 5% PEG 400, 0.2M NaCl, protein: 0.1mL protein, 0.3mL 2mM doxyTc, 0.001mL 3M MgCl2, 100mM NaCl, 50mM Tris, pH 8.0, Protein/precipitant 2/2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.378 | α = 90 |
b = 68.378 | β = 90 |
c = 180.008 | 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 | 100 | CCD | RIGAKU SATURN 70 | 2011-08-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.8 | 32.94 | 99.8 | 0.142 | 0.149 | 0.043 | 10.6 | 10.8 | 40487 | 24.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.8 | 1.9 | 98.9 | 0.935 | 1.052 | 0.467 | 2.1 | 4.7 |
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 | 5FKK | 1.8 | 31.98 | 38282 | 2039 | 99.43 | 0.21075 | 0.20905 | 0.24309 | RANDOM | 27.671 |
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] | |
0.3 | 0.3 | -0.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.633 |
r_dihedral_angle_4_deg | 20.953 |
r_dihedral_angle_3_deg | 13.956 |
r_dihedral_angle_1_deg | 6.038 |
r_long_range_B_refined | 5.527 |
r_long_range_B_other | 5.506 |
r_scangle_other | 3.288 |
r_mcangle_it | 3.005 |
r_mcangle_other | 3.004 |
r_scbond_other | 2.017 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3192 |
Nucleic Acid Atoms | |
Solvent Atoms | 262 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data reduction |
SCALA | data scaling |
REFMAC | phasing |