2IJ9
Crystal Structure of Uridylate Kinase from Archaeoglobus Fulgidus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BRX | PDB entry 2BRX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 294 | 100MM SODIUM CITRATE, PH 4.5, 3.5M AMMONIUM SULFATE, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.32 | 71.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.277 | α = 90 |
b = 94.277 | β = 90 |
c = 186.672 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | 100 | CCD | MARRESEARCH | MIRRORS | 2006-03-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97931 | APS | 31-ID |
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 | 2.6 | 50 | 87.6 | 0.093 | 0.081 | 6.3 | 6 | 23600 | 23600 |
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 | 2.6 | 2.69 | 54.5 | 0.502 | 0.78 | 0.5 | 1.4 | 1438 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2BRX | 2.9 | 20 | 17774 | 17774 | 595 | 95.09 | 0.28428 | 0.2828 | 0.33021 | RANDOM | 96.22 |
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] | |
2.73 | 2.73 | -5.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.073 |
r_scangle_it | 24.823 |
r_dihedral_angle_3_deg | 19.465 |
r_dihedral_angle_4_deg | 19.132 |
r_scbond_it | 17.963 |
r_mcangle_it | 12.32 |
r_mcbond_it | 8.564 |
r_dihedral_angle_1_deg | 7.897 |
r_angle_refined_deg | 1.377 |
r_nbtor_refined | 0.317 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3224 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |