3RHT
Crystal structure of type 1 glutamine amidotransferase (GATase1)-like protein from Planctomyces limnophilus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | 0.16 M calcium acetate, 0.08 M sodium cacodylate, 14.4% PEG8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.287 | α = 90 |
b = 126.827 | β = 96.6 |
c = 101.964 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CCD | ADSC QUANTUM 210r | mirrors | 2011-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97929 | APS | 19-BM |
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 | 1.83 | 50 | 99.9 | 0.093 | 19.5 | 3.8 | 93377 | 93329 | -3 | 18.7 |
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) | |||||||||||
1.83 | 1.86 | 99.6 | 0.607 | 2.4 | 3.3 | 4567 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SAD | THROUGHOUT | 1.83 | 50 | 93207 | 93207 | 1383 | 99.7 | 0.15803 | 0.15803 | 0.15754 | 0.19172 | RANDOM | 18.098 |
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] | |
-0.95 | -0.35 | 1.23 | -0.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.113 |
r_dihedral_angle_4_deg | 17.001 |
r_dihedral_angle_3_deg | 12.416 |
r_dihedral_angle_1_deg | 5.8 |
r_scangle_it | 3.693 |
r_scbond_it | 2.416 |
r_angle_refined_deg | 1.44 |
r_mcangle_it | 1.312 |
r_angle_other_deg | 0.937 |
r_mcbond_it | 0.766 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7752 |
Nucleic Acid Atoms | |
Solvent Atoms | 595 |
Heterogen Atoms | 73 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
SHELX | model building |
MLPHARE | phasing |
DM | model building |
ARP/wARP | model building |
Coot | model building |
PHENIX | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
SHELX | phasing |
DM | phasing |
PHENIX | phasing |