2H9W
Green fluorescent protein ground states: the influence of a second protonation site near the chromophore
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2H6V | PDB ENTRY 2H6V |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 298 | AS, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 42.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.886 | α = 90 |
b = 62.933 | β = 90 |
c = 71.035 | 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 | 298 | CCD | MARRESEARCH | 2006-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.979469 | ESRF | BM30A |
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 | 1.82 | 47.106 | 97.2 | 0.066 | 0.066 | 8.2 | 6.3 | 20710 | 20710 | 2 | 2 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.82 | 1.92 | 97.2 | 0.387 | 0.387 | 1.9 | 3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 2H6V | 1.82 | 47.09 | 2 | 20710 | 20710 | 1072 | 96.33 | 0.16732 | 0.16632 | 0.18594 | RANDOM | 19.482 |
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] | |
-0.69 | -0.14 | 0.83 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.932 |
r_dihedral_angle_3_deg | 13.291 |
r_dihedral_angle_4_deg | 11.754 |
r_dihedral_angle_1_deg | 6.402 |
r_scangle_it | 3.525 |
r_scbond_it | 2.645 |
r_angle_refined_deg | 1.578 |
r_mcangle_it | 1.561 |
r_mcbond_it | 1.428 |
r_angle_other_deg | 1.385 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1912 |
Nucleic Acid Atoms | |
Solvent Atoms | 109 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
CCP4 | model building |
REFMAC | refinement |
CCP4 | data scaling |
CCP4 | phasing |