2H8R
Hepatocyte Nuclear Factor 1b bound to DNA: MODY5 Gene Product
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IC8 | PDB ENTRY 1IC8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 295 | 6%(v/v) PEG300, 5%(v/v) PEG8000, 8%(v/v) glycerol, 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.32 | 62.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 174.689 | α = 90 |
b = 174.689 | β = 90 |
c = 72.434 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 225 mm CCD | 2005-12-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 0.97923 | APS | 22-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 3.2 | 27.9 | 93.9 | 0.088 | 0.083 | 28.8 | 6.3 | 12635 | 12582 | 57.24 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
3.2 | 3.31 | 63.4 | 0.313 | 0.273 | 3.35 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1IC8 | 3.2 | 20 | 2 | 12582 | 11992 | 637 | 93.26 | 0.22614 | 0.22292 | 0.19 | 0.2899 | 0.26 | RANDOM | 69.209 |
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] | |
5.43 | 2.72 | 5.43 | -8.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 20.239 |
r_dihedral_angle_1_deg | 12.042 |
r_scangle_it | 8.674 |
r_scbond_it | 5.745 |
r_angle_refined_deg | 5.45 |
r_sphericity_bonded | 5.174 |
r_mcangle_it | 4.678 |
r_rigid_bond_restr | 3.686 |
r_mcbond_it | 2.542 |
r_symmetry_hbond_refined | 0.47 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2916 |
Nucleic Acid Atoms | 814 |
Solvent Atoms | 7 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SERGUI | data collection |
HKL-2000 | data reduction |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data scaling |