1V1A
2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1V19 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 298 | VAPOUR-DIFFUSION SITTING DROP AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM KDG AND 5 MM AMP-PNP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M TRIS-HCL BUFFER, PH 8.5. BEFORE THE DATA COLLECTION THE CRYSTAL WAS SOAKED IN SOLUTION CONTAINING 0.35 M MAGNESIUM CHLORIDE INSTEAD OF AMMONIUM SULFATE. THE CRYOPROTECTANT CONTAINED 33% OF ETHYLENE GLYCOL IN ADDITION TO MAGNESIUM CHLORIDE, BUFFER AND LIGANDS |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 52.5 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 84.321 | ¦Á = 90 |
b = 84.321 | ¦Â = 90 |
c = 168.701 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 63 |
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 | IMAGE PLATE | RIGAKU IMAGE PLATE R-AXISV | 2003-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | SPring-8 | BL26B1 |
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 | 30 | 97.9 | 0.056 | 19.6 | 4.58 | 38730 | -0.4 | 13.1 |
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 | 2.18 | 96.2 | 0.355 | 2.68 |
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 V19 | 2.1 | 29.82 | 37822 | 1852 | 95.7 | 0.1798 | 0.1798 | 0.2677 | RANDOM | 51.4 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-3.709 | -3.064 | -3.709 | 7.417 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23 |
c_scangle_it | 11.51 |
c_scbond_it | 8.64 |
c_mcangle_it | 8.46 |
c_mcbond_it | 5.94 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.85 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4594 |
Nucleic Acid Atoms | |
Solvent Atoms | 211 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |