2J4J
Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP and AMPPCP to 2.1 Angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BMU | PDB ENTRY 2BMU - WITHOUT LIGANDS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK AND 2MM UMP. 2MM AMPPCP AND 5 MM MGCL2 MIXED WITH 2 UL MOTHER SOLUTION. MOTHER SOLUTION: 0.8 M 1,6-HEXANEDIOL, 5 MM COCL2, AND 0.1 M SODIUM ACETATE, PH 4.6. HANGING DROP VAPOR DIFFUSION TECHNIQUE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 46.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.174 | α = 90 |
b = 126.438 | β = 90 |
c = 134.991 | 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 | MARRESEARCH | VERTICALLY FOCUSING CYLINDRICAL MIRROR | 2004-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I711 | MAX II | I711 |
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 | 91.29 | 99.9 | 0.1 | 6 | 6.7 | 86630 | -3 |
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 | 2.1 | 2.21 | 99.9 | 0.5 | 1.4 | 6.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 2BMU - WITHOUT LIGANDS | 2.1 | 25 | 82168 | 4353 | 100 | 0.216 | 0.215 | 0.242 | RANDOM | 28.37 |
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] | |
0.89 | 0.79 | -1.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.747 |
r_dihedral_angle_4_deg | 22.743 |
r_dihedral_angle_3_deg | 16.049 |
r_dihedral_angle_1_deg | 5.963 |
r_scangle_it | 2.852 |
r_scbond_it | 1.949 |
r_angle_refined_deg | 1.559 |
r_mcangle_it | 1.445 |
r_mcbond_it | 1.316 |
r_angle_other_deg | 0.889 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10212 |
Nucleic Acid Atoms | |
Solvent Atoms | 337 |
Heterogen Atoms | 319 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |