2NXP
Structure of NTD2 domain of the human TAF5 subunit of TFIID
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.1 | 295 | 0.1M Tris-HCl, 0.6M calcium chloride, 20% PEG 4000, pH 7.1, VAPOR DIFFUSION, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.62 | α = 90 |
b = 61.829 | β = 105.16 |
c = 133.357 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | CCD | ADSC QUANTUM 210 | KOHZU: Double Crystal Si(111) | 2005-10-25 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 0.9797, 1.0199 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.2 | 64.4 | 97.8 | 0.102 | 9.3 | 4.3 | 78392 | 76736 | 2 | 2 | 38.2 |
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) | |||||||||||
2.2 | 97.9 | 0.065 | 2.5 | 4.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MAD | THROUGHOUT | 2.17 | 64.42 | 76736 | 72912 | 3837 | 97.89 | 0.21507 | 0.21257 | 0.26252 | RANDOM | 35.522 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.441 |
r_dihedral_angle_3_deg | 12.129 |
r_dihedral_angle_4_deg | 10.597 |
r_dihedral_angle_1_deg | 4.379 |
r_angle_refined_deg | 0.722 |
r_angle_other_deg | 0.6 |
r_symmetry_vdw_refined | 0.234 |
r_symmetry_vdw_other | 0.221 |
r_symmetry_hbond_refined | 0.221 |
r_nbd_refined | 0.212 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9986 |
Nucleic Acid Atoms | |
Solvent Atoms | 521 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
MOSFLM | data reduction |
CCP4 | data scaling |
MLPHARE | phasing |