6RYM
Structure of carbohydrate recognition domain with GlcNAc bound
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | 2.5 M ammonium sulfate, 0.1 M tris |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.225 | α = 90 |
b = 50.225 | β = 90 |
c = 51.925 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
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 | MAR CCD 165 mm | 2004-06-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX10.1 | 1.488 | SRS | PX10.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.457 | 25.106 | 80.8 | 0.036 | 0.036 | 0.054 | 31.5 | 6.5 | 18321 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.46 | 1.54 | 21.8 | 0.121 | 0.121 | 0.186 | 2.8 | 2.6 |
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 | pdbid 6RYJ | 1.46 | 25.106 | 17355 | 945 | 80.79 | 0.1625 | 0.1614 | 0.1841 | RANDOM | 14.2 |
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] | |
-0.23 | -0.23 | 0.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.414 |
r_dihedral_angle_4_deg | 19.271 |
r_dihedral_angle_3_deg | 11.027 |
r_dihedral_angle_1_deg | 6.704 |
r_angle_refined_deg | 1.38 |
r_angle_other_deg | 0.974 |
r_chiral_restr | 0.068 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.008 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 940 |
Nucleic Acid Atoms | |
Solvent Atoms | 149 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
REFMAC | phasing |