1B7Y
PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PYS | PDB ENTRY 1PYS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 313 | HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED (NH4)2SO4 IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO THE MAXIMAL DIMENSIONS OF 0.4X0.4X0.25 MM IN A FEW WEEKS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 70 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 174.5 | α = 90 |
b = 174.5 | β = 90 |
c = 140.2 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | IMAGE PLATE | RIGAKU | 1998-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | SPring-8 | BL41XU |
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 | 2.5 | 50 | 95.7 | 0.064 | 6 | 4 | 81613 | 81613 | 45 |
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 | 2.5 | 2.59 | 88.5 | 0.399 | 2.2 | 4 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1PYS | 2.5 | 50 | 81613 | 81613 | 4000 | 95.7 | 0.23 | 0.267 | RANDOM | 62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 25 |
x_scangle_it | 8.5 |
x_scbond_it | 6 |
x_mcangle_it | 5.2 |
x_mcbond_it | 3.7 |
x_angle_deg | 1.72 |
x_improper_angle_d | 0.83 |
x_bond_d | 0.01 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8166 |
Nucleic Acid Atoms | |
Solvent Atoms | 239 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |