2RAV
X-ray Crystallographic Structures Show Conservation of a Trigonal-Bipyramidal Intermediate in a Phosphoryl-transfer Superfamily.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 15%PEG 1500, 10mM magnesium chloride and 5mM sodium tungstate., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.94 | 45.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.526 | α = 90 |
b = 56.339 | β = 90 |
c = 93.77 | 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 | 100 | CCD | ADSC QUANTUM 210 | mirrors | 2005-09-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | 0.9000 | NSLS | X12C |
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 | 1.07 | 50 | 98 | 0.083 | 0.083 | 21.2 | 8 | 114002 | 114002 | 2 | 2 | 8.8 |
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 | 1.07 | 1.11 | 91.6 | 0.501 | 0.028 | 0.028 | 3.7 | 10529 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | AB INITIO | FREE R | 1YMQ | 1.07 | 10 | 2 | 113636 | 113636 | 11375 | 98 | 0.1169 | 0.1169 | 0.1169 | 0.1489 | RANDOM | 18.4 |
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] | |
1.66 | -0.71 | -0.95 |
Coordinate Error | ||
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Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
16 | 1751 | 2548 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.109 |
s_non_zero_chiral_vol | 0.084 |
s_zero_chiral_vol | 0.076 |
s_similar_adp_cmpnt | 0.034 |
s_angle_d | 0.031 |
s_from_restr_planes | 0.0276 |
s_anti_bump_dis_restr | 0.02 |
s_bond_d | 0.015 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2022 |
Nucleic Acid Atoms | |
Solvent Atoms | 520 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
CBASS | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |