3PTQ
The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 288.15 | 19% PEG 2000, 0.1M Tris HCl, 0.16M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.13 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 114.112 | ¦Á = 90 |
b = 114.112 | ¦Â = 90 |
c = 184.541 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2008-06-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 1.0000 | NSRRC | BL13B1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.45 | 30 | 99.9 | 0.094 | 4.4 | 8.6 | 43131 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.45 | 2.51 | 99.9 | 0.49 | 4.4 | 8.6 | 381316 |
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 | Native Os4BGlu12 | 2.45 | 30 | 43131 | 2292 | 99.81 | 0.21113 | 0.20903 | 0.25065 | RANDOM | 33.562 |
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] | |
0.51 | 0.51 | -1.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.384 |
r_dihedral_angle_4_deg | 20.182 |
r_dihedral_angle_3_deg | 17.585 |
r_dihedral_angle_1_deg | 7.509 |
r_mcangle_it | 2.145 |
r_scangle_it | 1.885 |
r_mcbond_it | 1.831 |
r_angle_refined_deg | 1.264 |
r_scbond_it | 1.162 |
r_nbtor_refined | 0.312 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7722 |
Nucleic Acid Atoms | |
Solvent Atoms | 280 |
Heterogen Atoms | 79 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |