3MTR
Crystal structure of the Ig5-FN1 tandem of human NCAM
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2HAZ | PDB entry 2HAZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 295 | 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.09 | α = 90 |
b = 155.84 | β = 90 |
c = 71.75 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | CCD | MARMOSAIC 225 mm CCD | 2008-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0 | APS | 22-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.79 | 30 | 98.7 | 0.095 | 14.92 | 40353 | 1 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.79 | 1.9 | 96.3 | 0.585 | 6.11 | 6259 |
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 and ARP | THROUGHOUT | PDB entry 2HAZ | 1.8 | 30 | 35851 | 35851 | 4060 | 98.69 | 0.18816 | 0.18816 | 0.18343 | 0.23022 | RANDOM | 23.848 |
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] | |
1.01 | -0.24 | -0.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.501 |
r_dihedral_angle_4_deg | 13.602 |
r_dihedral_angle_3_deg | 12.724 |
r_dihedral_angle_1_deg | 6.684 |
r_scangle_it | 3.98 |
r_scbond_it | 2.639 |
r_angle_refined_deg | 1.567 |
r_mcangle_it | 1.53 |
r_mcbond_it | 0.991 |
r_nbtor_refined | 0.311 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3018 |
Nucleic Acid Atoms | |
Solvent Atoms | 340 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
MOLREP | phasing |
PHASER | phasing |
ARP | model building |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |