3KUU
Structure of the PurE Phosphoribosylaminoimidazole Carboxylase Catalytic Subunit from Yersinia pestis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 1.6M ammonium sulphate, 4% maltose, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 114.04 | α = 90 |
b = 114.04 | β = 90 |
c = 231.74 | γ = 90 |
Symmetry | |
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Space Group | I 4 2 2 |
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 | 110 | CCD | MARMOSAIC 300 mm CCD | bimorph KB mirrors | 2009-11-13 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 110 | CCD | MARMOSAIC 300 mm CCD | bimorph KB mirrors | 2009-11-12 | M | SINGLE WAVELENGTH | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.127 | APS | 21-ID-D |
2 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.9763 | APS | 21-ID-D |
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 | 1.4 | 50 | 99.1 | 0.104 | 14.2 | 11.8 | 147075 | 145751 | 1.7 | 3 |
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 | 1.4 | 1.45 | 93.5 | 0.518 | 3 | 5.7 | 13631 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.41 | 34.3 | 3 | 147010 | 145702 | 7296 | 99.11 | 0.151 | 0.151 | 0.15 | 0.167 | RANDOM | 12.154 |
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] | |
-0.01 | -0.01 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.17 |
r_dihedral_angle_4_deg | 20.262 |
r_dihedral_angle_3_deg | 11.082 |
r_scangle_it | 5.727 |
r_dihedral_angle_1_deg | 5.361 |
r_scbond_it | 3.669 |
r_mcangle_it | 2.233 |
r_angle_refined_deg | 1.631 |
r_mcbond_it | 1.416 |
r_chiral_restr | 0.113 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4837 |
Nucleic Acid Atoms | |
Solvent Atoms | 861 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
BLU-MAX | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |