5OLR
Rhamnogalacturonan lyase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 100 mM succinic acid, sodium phosphate glycine buffer pH 6.0 and 25 % (w/v) PEG 1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.93 | 36.31 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 77.458 | ¦Á = 90 |
b = 123.872 | ¦Â = 90 |
c = 137.628 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 2014-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97949 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.07 | 48.4 | 94.3 | 0.998 | 11.3 | 3.2 | 536956 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.07 | 1.09 | 33.1 | 0.378 | 0.9 | 1.7 |
Refinement
Statistics | |||||||||||||||||||
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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 | THROUGHOUT | 1.07 | 48.4 | 509939 | 26889 | 94.32 | 0.1458 | 0.1447 | 0.16643 | RANDOM | 11.582 |
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] | |
0.11 | -0.31 | 0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.516 |
r_sphericity_free | 23.039 |
r_dihedral_angle_4_deg | 11.861 |
r_dihedral_angle_3_deg | 10.866 |
r_sphericity_bonded | 7.352 |
r_dihedral_angle_1_deg | 7.217 |
r_rigid_bond_restr | 4.915 |
r_long_range_B_refined | 3.443 |
r_long_range_B_other | 3.443 |
r_scangle_other | 1.822 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9788 |
Nucleic Acid Atoms | |
Solvent Atoms | 1757 |
Heterogen Atoms | 126 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
Coot | model building |