3QLQ
Crystal structure of Concanavalin A bound to an octa-alpha-mannosyl-octasilsesquioxane cluster
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SCR | PDB ENTRY 1SCR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 294.15 | 12% PEG 2K MME, 1mM Manganese Chloride, 1mM Calcium Chloride, 100mM HEPES pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.89 | α = 90 |
b = 63.68 | β = 93.23 |
c = 125.8 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 270 | TOROIDAL FOCUSING MIRROR | 2010-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.95370 | NSLS | X6A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.7 | 31.84 | 96.1 | 0.076 | 13.9 | 6.2 | 104059 | 100001 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.7 | 1.79 | 88 | 0.657 | 2.3 | 5.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1SCR | 1.7 | 31.84 | 98996 | 94987 | 4961 | 95.95 | 0.21942 | 0.21942 | 0.21783 | 0.24832 | RANDOM | 20.338 |
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] | |
-1.18 | 0.01 | 3.12 | -1.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.03 |
r_dihedral_angle_4_deg | 16.61 |
r_dihedral_angle_3_deg | 14.351 |
r_dihedral_angle_1_deg | 7.703 |
r_scangle_it | 4.417 |
r_scbond_it | 2.942 |
r_mcangle_it | 2.206 |
r_angle_refined_deg | 1.986 |
r_mcbond_it | 1.312 |
r_angle_other_deg | 1.04 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7111 |
Nucleic Acid Atoms | |
Solvent Atoms | 253 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |