2CGZ
Structure of Helix Pomatia agglutinin with Tn antigen
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CE6 | PDB ENTRY 2CE6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | HANGING DROP METHOD WITH PRECIPITATION SOLUTION CONTAINING LITHIUM SULPHATE (2 M) AND AMMONIUM SULPHATE (3.5 M) IN SODIUM CITRATE BUFFER (1.5M, PH 6.5) AND 10MM TN ANTIGEN. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 47 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 62.1 | ¦Á = 90 |
b = 62.1 | ¦Â = 90 |
c = 106.2 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 63 2 2 |
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 CCD | MIRROR | 2000-04-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 2.8 | 30 | 93.1 | 0.05 | 19.2 | 7.3 | 3132 |
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 | 2.8 | 2.9 | 95.2 | 0.36 | 4.6 |
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 | PDB ENTRY 2CE6 | 2.8 | 20 | 2958 | 130 | 93.3 | 0.244 | 0.242 | 0.29 | RANDOM | 64.46 |
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] | |
-3.6 | -1.8 | -3.6 | 5.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.239 |
r_angle_refined_deg | 1.004 |
r_scangle_it | 1.004 |
r_angle_other_deg | 0.698 |
r_mcangle_it | 0.577 |
r_scbond_it | 0.545 |
r_symmetry_vdw_refined | 0.387 |
r_mcbond_it | 0.31 |
r_symmetry_vdw_other | 0.214 |
r_nbd_other | 0.197 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 774 |
Nucleic Acid Atoms | |
Solvent Atoms | 7 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |