6RYN
Structure of conglutinin carbohydrate recognition domain with GlcNAc-alpha-1-phosphate 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 |
2.34 | 47.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.278 | α = 90 |
b = 50.278 | β = 90 |
c = 52.192 | 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 | ADSC QUANTUM 315 | 2009-05-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.827 | Diamond | I04 |
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 | 50.304 | 99.7 | 0.04 | 0.04 | 0.047 | 20.7 | 7.7 | 70085 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1 | 99.9 | 0.389 | 0.389 | 0.463 | 2 | 7.4 |
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 | 50 | 66521 | 3523 | 99.46 | 0.1247 | 0.1239 | 0.14 | RANDOM | 13.161 |
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] | |
-0.03 | -0.03 | 0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.078 |
r_dihedral_angle_4_deg | 18.139 |
r_dihedral_angle_3_deg | 10.685 |
r_rigid_bond_restr | 9.814 |
r_dihedral_angle_1_deg | 6.427 |
r_angle_refined_deg | 1.783 |
r_angle_other_deg | 1.587 |
r_chiral_restr | 0.091 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 905 |
Nucleic Acid Atoms | |
Solvent Atoms | 173 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
REFMAC | phasing |