4PSB
Crystal Structure of Phytohormone Binding Protein from Vigna radiata in complex with gibberellic acid (GA3)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 292 | 0.1 M MMT buffer pH 4.0, 25% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.86 | 33.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 34.38 | α = 90 |
b = 54.29 | β = 98.7 |
c = 71.09 | 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 PILATUS 6M | mirrors | 2013-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.97551 | PETRA III, EMBL c/o DESY | P14 (MX2) |
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 | 1.42 | 35.14 | 99.5 | 0.079 | 9.2 | 4.9 | 24476 | 24350 | -3 | 18.06 |
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 | 1.42 | 1.46 | 99.3 | 0.52 | 1.98 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 2FLH | 1.42 | 35.14 | 24476 | 24350 | 1023 | 99.5 | 0.1543 | 0.152 | 0.2039 | 24.53 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.854 |
f_angle_d | 1.911 |
f_chiral_restr | 0.125 |
f_bond_d | 0.019 |
f_plane_restr | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1225 |
Nucleic Acid Atoms | |
Solvent Atoms | 140 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MxCuBE | data collection |
XDS | data reduction |
PHASER | phasing |