6VBH
Human XPG endonuclease catalytic domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 288 | Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2 | |
2 | VAPOR DIFFUSION, HANGING DROP | 288 | Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT | |
3 | VAPOR DIFFUSION, HANGING DROP | 288 | Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.438 | α = 90 |
b = 173.403 | β = 90 |
c = 101.608 | γ = 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 | CCD | ADSC QUANTUM 315 | 2010-07-08 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | 2010-07-24 | M | SINGLE WAVELENGTH | ||||||
3 | 3 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | 2010-07-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 12.3.1 | 1.115953 | ALS | 12.3.1 |
2 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 1.1 | SSRL | BL11-1 |
3 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 1.1 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.995 | 50 | 92.2 | 0.122 | 0.125 | 0.029 | 11.6 | 13.4 | 36003 | 42.97 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2 | 2.03 | 66.5 | 0.725 | 0.797 | 0.319 | 0.814 | 4.5 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3q8k | 1.995 | 43.833 | 32323 | 1602 | 82.55 | 0.2211 | 0.2198 | 0.2444 | 80.6006 |
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 | 9.051 |
f_angle_d | 1.249 |
f_chiral_restr | 0.062 |
f_bond_d | 0.013 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2672 |
Nucleic Acid Atoms | |
Solvent Atoms | 119 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |