7LSC
Crystal structure of near-infrared fluorescent protein miRFP670nano3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.3 | 293 | 8.4% PEG4000, 3.6% MPD, 0.06 M sodium/potassium phosphate, pH 6.3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.531 | α = 90 |
b = 73.953 | β = 101.71 |
c = 83.743 | 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 | PIXEL | DECTRIS EIGER X 16M | 2020-02-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
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) | 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 | 1.8 | 30 | 98.5 | 0.074 | 0.083 | 0.037 | 9.8 | 4.5 | 60575 |
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 | 1.8 | 1.86 | 93.6 | 0.815 | 0.935 | 0.446 | 0.682 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 6MGH | 1.8 | 29.83 | 59390 | 1185 | 98.21 | 0.1789 | 0.1778 | 0.2371 | RANDOM | 38.314 |
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] | |
0.3 | -2.14 | -0.32 | 0.83 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.225 |
r_dihedral_angle_4_deg | 17.125 |
r_dihedral_angle_3_deg | 15.727 |
r_dihedral_angle_1_deg | 7.707 |
r_angle_refined_deg | 2.283 |
r_angle_other_deg | 1.534 |
r_chiral_restr | 0.096 |
r_gen_planes_refined | 0.011 |
r_gen_planes_other | 0.011 |
r_bond_refined_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4940 |
Nucleic Acid Atoms | |
Solvent Atoms | 371 |
Heterogen Atoms | 172 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
MOLREP | phasing |