4GES
crystal structure of GFP-TYR151PYZ with an unnatural amino acid incorporation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GFL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.9 | 289 | 60~100mg/ml protein sample in 50 mM Hepes, pH 7.5, reservior solution:16~19% PEG 3000, 100mM Tris pH 8.9,0.2M calcium acetate, VAPOR DIFFUSION, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.717 | α = 90 |
b = 50.809 | β = 90 |
c = 62.364 | 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 | 90 | CCD | ADSC QUANTUM 315 | 2012-01-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.979 | SSRF | BL17U |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.23 | 50 | 98.7 | 0.09 | 0.077 | 23.5 | 9.5 | 63375 | 62551 | 3 | 3 |
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 | THROUGHOUT | 1GFL | 1.23 | 45.87 | 59944 | 59267 | 3167 | 98.87 | 0.17 | 0.16414 | 0.16293 | 0.18773 | RANDOM | 13.004 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.82 | -0.84 | -0.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.42 |
r_dihedral_angle_3_deg | 11.22 |
r_dihedral_angle_1_deg | 10.562 |
r_dihedral_angle_4_deg | 8.929 |
r_sphericity_free | 5.137 |
r_scangle_it | 3.491 |
r_sphericity_bonded | 2.795 |
r_scbond_it | 2.339 |
r_mcangle_it | 1.766 |
r_angle_refined_deg | 1.474 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1813 |
Nucleic Acid Atoms | |
Solvent Atoms | 206 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
HKL-2000 | data collection |
DENZO | data reduction |
HKL-2000 | data scaling |
CNS | phasing |