4W7U
Crystal structure of XacCel5A in the native form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | 0.1 M sodium cacodylate, 0.2 M sodium acetate, 28% PEG8000, 5% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.367 | α = 90 |
b = 81.73 | β = 90 |
c = 48.232 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | MARMOSAIC 225 mm CCD | 2013-08-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.459 | LNLS | W01B-MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.48 | 41.54 | 99.1 | 0.094 | 0.111 | 7.41 | 3.5 | 100540 | -3 | 24.242 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.48 | 1.57 | 96.5 | 1.19 | 1.19 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1GZJ | 1.48 | 41.54 | 50433 | 2548 | 99.56 | 0.1461 | 0.1437 | 0.1931 | RANDOM | 20.611 |
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] | |
-0.58 | -0.45 | 1.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.439 |
r_sphericity_free | 37.143 |
r_dihedral_angle_4_deg | 26.425 |
r_dihedral_angle_3_deg | 13.237 |
r_sphericity_bonded | 11.613 |
r_dihedral_angle_1_deg | 6.084 |
r_mcangle_it | 2.967 |
r_rigid_bond_restr | 2.695 |
r_mcbond_it | 2.43 |
r_mcbond_other | 2.366 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2447 |
Nucleic Acid Atoms | |
Solvent Atoms | 215 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |