6YXM
Crystal structure of ACPA 1F2 in complex with CII-C-39-CIT
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 20mM Tris pH 7.4, 20mMNaCl, 20% (w/v) PEG 6000, 0.1M HEPES 7.0 pH 7.0, 0.01M zinc chloride. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.01 | α = 90 |
b = 89.65 | β = 90 |
c = 118.68 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 210 | PIXEL | DECTRIS PILATUS3 6M | 2018-03-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97662 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.85 | 118.75 | 99.9 | 0.146 | 0.165 | 0.076 | 0.993 | 9.9 | 8.8 | 13893 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.85 | 3 | 0.501 | 0.569 | 0.267 | 0.914 | 8.7 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5ocx | 2.85 | 36.219 | 13539 | 638 | 98.137 | 0.213 | 0.2098 | 0.2762 | 39.044 |
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] | |
-0.81 | 0.63 | 0.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.407 |
r_dihedral_angle_4_deg | 17.154 |
r_dihedral_angle_3_deg | 16.446 |
r_dihedral_angle_1_deg | 8.123 |
r_lrange_it | 2.348 |
r_lrange_other | 2.345 |
r_angle_refined_deg | 1.333 |
r_mcangle_it | 1.143 |
r_mcangle_other | 1.143 |
r_angle_other_deg | 1.122 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3275 |
Nucleic Acid Atoms | |
Solvent Atoms | 33 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
Aimless | data reduction |
XDS | data reduction |
Coot | model building |