5HXY
Crystal structure of XerA recombinase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 295.5 | PEG 4000, ADA, LiSO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 182.86 | α = 90 |
b = 105.968 | β = 110.01 |
c = 115.586 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2008-03-03 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 0.97952, 0.97987, 0.9800 | Photon Factory | BL-5A |
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 | 2.5 | 50 | 95.4 | 13.69 | 3.3 | 68638 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.5 | 47.66 | 65159 | 3479 | 95.25 | 0.19129 | 0.18847 | 0.24321 | RANDOM | 33.442 |
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] | |
-0.57 | 0.25 | -1.04 | 1.2 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.931 |
r_dihedral_angle_4_deg | 18.947 |
r_dihedral_angle_3_deg | 18.504 |
r_long_range_B_refined | 6.5 |
r_long_range_B_other | 6.368 |
r_dihedral_angle_1_deg | 6.171 |
r_scangle_other | 4.305 |
r_mcangle_it | 3.67 |
r_mcangle_other | 3.67 |
r_scbond_it | 2.785 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13501 |
Nucleic Acid Atoms | |
Solvent Atoms | 491 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data collection |
HKL-2000 | data scaling |
SOLVE | phasing |
RESOLVE | model building |
PDB_EXTRACT | data extraction |