3MJF
Phosphoribosylamine-glycine ligase from Yersinia pestis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% PEG-8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.637 | α = 90 |
b = 69.151 | β = 90 |
c = 95.166 | 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 210r | 2010-04-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9792 | 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 | 1.47 | 30.8 | 99.9 | 0.097 | 12.9 | 9.5 | 77813 | 77813 | 24.4 |
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) | |||||||||||
1.47 | 1.5 | 99.8 | 0.883 | 3.05 | 9.1 | 3850 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1.47 | 30.8 | 77708 | 77708 | 3907 | 99.67 | 0.137 | 0.137 | 0.135 | 0.174 | RANDOM | 19.157 |
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] | |
0.39 | -0.01 | -0.38 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.225 |
r_dihedral_angle_4_deg | 22.783 |
r_dihedral_angle_3_deg | 13.873 |
r_scangle_it | 6.364 |
r_dihedral_angle_1_deg | 5.744 |
r_scbond_it | 4.374 |
r_mcangle_it | 2.829 |
r_mcbond_it | 1.911 |
r_rigid_bond_restr | 1.794 |
r_angle_refined_deg | 1.74 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3192 |
Nucleic Acid Atoms | |
Solvent Atoms | 512 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SBC-Collect | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
SHELXD | phasing |
MLPHARE | phasing |
DM | phasing |
SOLVE | phasing |
RESOLVE | phasing |
HKL-3000 | phasing |