2WYQ
THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BWF | PDB ENTRY 2BWF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 0.1 M HEPES PH 7.5, 2% PEG 400 AND 2.0 M AMMONIUM SULFATE, AT ROOM TEMPERATURE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.434 | α = 90 |
b = 78.434 | β = 90 |
c = 63.472 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 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 | ADSC CCD | 2009-09-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 1.65 | 63.57 | 100 | 0.08 | 5.86 | 36.17 | 14363 | 2 | 21.4 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1 | 1.65 | 1.74 | 100 | 0.35 | 2.08 | 23 |
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 | PDB ENTRY 2BWF | 1.651 | 35 | 14330 | 706 | 99.902 | 0.126 | 0.1241 | 0.1598 | RANDOM | 9.296 |
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] | |
0.026 | 0.013 | 0.026 | -0.039 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.598 |
r_dihedral_angle_4_deg | 22.156 |
r_sphericity_free | 20.126 |
r_dihedral_angle_3_deg | 14.992 |
r_scangle_it | 7.41 |
r_dihedral_angle_1_deg | 6.351 |
r_sphericity_bonded | 5.566 |
r_scbond_it | 5.423 |
r_mcangle_it | 3.553 |
r_angle_other_deg | 3.113 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 603 |
Nucleic Acid Atoms | |
Solvent Atoms | 108 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |