6HFF
Human dihydroorotase mutant F1563Y apo structure
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4C6C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | Protein at 2-3 mg/ml in 20 mM Tris pH 8, 0.15 M NaCl, 0.02 mM zinc sulfate, 0.2 mM TCEP Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.89 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 81.73 | ¦Á = 90 |
b = 159.2 | ¦Â = 90 |
c = 61.06 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | PIXEL | DECTRIS PILATUS 6M | 2014-01-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.9795 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | 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 | 1.51 | 33.3423323303 | 99.87 | 0.05609 | 0.998 | 20.75 | 6.6 | 62752 | 19.6916122694 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.51 | 1.564 | 99.86 | 0.6614 | 0.92 | 3.83 | 6.7 |
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 (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4c6c | 1.51000106105 | 33.3423323303 | 1.00989222547 | 62752 | 6000 | 99.5945990668 | 0.127393544248 | 0.126137911629 | 0.151042799113 | 28.9715976065 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.4135815615 |
f_angle_d | 1.18362428288 |
f_chiral_restr | 0.17877882934 |
f_bond_d | 0.0106133567661 |
f_plane_restr | 0.0079516478724 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2789 |
Nucleic Acid Atoms | |
Solvent Atoms | 308 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |