6UHN
Crystal Structure of C148 mGFP-cDNA-1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5N9O |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 295 | 1 microliter C148 mGFP-cDNA-1 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.2 M lithium sulfate, 0.1 M Bis-Tris Buffer pH 5.5, 25% (w/v) PEG 3350) in a sitting drop with a 70 microliter reservoir 0.2 M lithium sulfate, 0.1 M Bis-Tris Buffer pH 5.5, 25% (w/v) PEG 3350) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.92 | α = 90 |
b = 52.18 | β = 94.24 |
c = 86.469 | 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 | RAYONIX MX-300 | 2019-03-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.92 | 86.233 | 100 | 0.112 | 0.129 | 0.063 | 7.8 | 4.3 | 44394 | 44394 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.92 | 2.02 | 99.9 | 0.442 | 0.442 | 0.507 | 0.244 | 3.1 | 4.3 |
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 | 5N9O | 1.92 | 53.72 | 42169 | 2208 | 99.94 | 0.2179 | 0.2164 | 0.2476 | RANDOM | 22.057 |
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] | |
0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.263 |
r_dihedral_angle_3_deg | 13.34 |
r_dihedral_angle_4_deg | 9.346 |
r_dihedral_angle_1_deg | 7.558 |
r_angle_refined_deg | 1.832 |
r_angle_other_deg | 1.397 |
r_chiral_restr | 0.072 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.01 |
r_gen_planes_other | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3466 |
Nucleic Acid Atoms | |
Solvent Atoms | 197 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |