2GK6
Structural and Functional insights into the human Upf1 helicase core
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GJK |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 7.5 | 295 | 100mM Tris, 8-13% PEG3350, 140mM (NH4)3PO4, 10% EG, 10mM DTT, pH 7.5, EVAPORATION, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.284 | α = 114.41 |
b = 67.836 | β = 90.13 |
c = 87.25 | γ = 110.22 |
Symmetry | |
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Space Group | P 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 | 100 | CCD | MAR CCD 165 mm | 2005-03-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.9793 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.4 | 20 | 90.8 | 43423 |
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 | 2GJK | 2.4 | 20 | 41163 | 2207 | 90.88 | 0.23709 | 0.2352 | 0.27193 | RANDOM | 32.418 |
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] | |
-0.97 | 1.53 | 1.21 | 3.32 | 2.56 | 0.83 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.145 |
r_scangle_it | 1.657 |
r_angle_refined_deg | 1.126 |
r_scbond_it | 0.944 |
r_mcangle_it | 0.922 |
r_angle_other_deg | 0.79 |
r_mcbond_it | 0.487 |
r_symmetry_hbond_refined | 0.243 |
r_symmetry_vdw_other | 0.224 |
r_nbd_other | 0.217 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9496 |
Nucleic Acid Atoms | |
Solvent Atoms | 233 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
CCP4 | data scaling |
AMoRE | phasing |