6MBX
CRYSTAL STRUCTURE OF MUSKMELON ALLERGEN CUC M 2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5EM0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 2.8M sodium acetate trihydrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.608 | α = 90 |
b = 59.237 | β = 90.02 |
c = 82.911 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 210r | 2018-07-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97933 | APS | 19-BM |
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) | Rpim 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 | 2.4 | 40 | 99.2 | 0.037 | 0.037 | 0.042 | 0.026 | 31.8 | 2.5 | 19535 | -3 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.4 | 2.44 | 100 | 0.309 | 0.309 | 0.607 | 0.368 | 0.876 | 2.3 | 2.5 |
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 | 5em0 | 2.4 | 32.26 | 18524 | 990 | 99.16 | 0.23256 | 0.23093 | 0.2611 | RANDOM | 94.246 |
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] | |
-4.99 | 1.72 | 1.1 | 3.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.775 |
r_dihedral_angle_4_deg | 29.421 |
r_dihedral_angle_3_deg | 13.667 |
r_dihedral_angle_1_deg | 8.132 |
r_long_range_B_refined | 4.219 |
r_long_range_B_other | 4.21 |
r_mcangle_it | 1.493 |
r_mcangle_other | 1.493 |
r_scangle_other | 1.389 |
r_angle_refined_deg | 1.294 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2889 |
Nucleic Acid Atoms | |
Solvent Atoms | 24 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SBC-Collect | data collection |
HKL-3000 | data scaling |
HKL-3000 | phasing |
MOLREP | phasing |
BUCCANEER | model building |
HKL-2000 | data processing |