4HHD
2.75 Angstrom resolution crystal structure of the A. thaliana LOV2 domain with an extended N-terminal A' helix (cryo dark structure)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2V0U | PDB ENTRY 2V0U |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 287 | Protein at 21 mg/mL in 20 mM TRIS-HCl pH 7.4, 20 mM NaCl, 15 % glycerol Crystallization: The JCSG+ Suite (D12: 0.04 M Potassium phosphate, 16% (w/v) PEG 8000, 20% (v/v) glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 287K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.382 | α = 90 |
b = 63.382 | β = 90 |
c = 171.318 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | 105 | CCD | ADSC QUANTUM 315 | Bent conical Si-mirror (Rh coated) | 2007-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 0.9002 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.75 | 30 | 87.9 | 0.07 | 17.5 | 3.3 | 8574 | 8574 | -3 | 66.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.75 | 2.8 | 86.6 | 0.585 | 2.2 | 3.6 | 399 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2V0U | 2.75 | 29.72 | 8128 | 8128 | 417 | 88.18 | 0.23399 | 0.23109 | 0.2894 | RANDOM | 48.442 |
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] | |
-1.75 | -1.75 | 3.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 23.087 |
r_dihedral_angle_3_deg | 9.903 |
r_dihedral_angle_4_deg | 7.057 |
r_dihedral_angle_1_deg | 2.771 |
r_scangle_it | 1.787 |
r_angle_refined_deg | 1.312 |
r_scbond_it | 1.071 |
r_angle_other_deg | 0.849 |
r_mcangle_it | 0.8 |
r_mcbond_it | 0.421 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2466 |
Nucleic Acid Atoms | |
Solvent Atoms | 29 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |