2C49
Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 15% PEG4000, 0.10 M MGCL2, 0.1 M TRIS-HCL PH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.006 | α = 90 |
b = 83.131 | β = 90 |
c = 146.784 | 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 CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 |
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 | 1.93 | 20 | 97 | 0.06 | 20 | 13.7 | 58526 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.92 | 72.55 | 55509 | 2955 | 97.1 | 0.245 | 0.243 | 0.281 | RANDOM | 21.37 |
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] | |
0.39 | 1.26 | -1.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 7.538 |
r_scangle_it | 2.989 |
r_scbond_it | 2.072 |
r_angle_refined_deg | 1.7 |
r_mcangle_it | 1.264 |
r_mcbond_it | 0.758 |
r_nbd_refined | 0.211 |
r_symmetry_vdw_refined | 0.196 |
r_xyhbond_nbd_refined | 0.159 |
r_symmetry_hbond_refined | 0.128 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4731 |
Nucleic Acid Atoms | |
Solvent Atoms | 162 |
Heterogen Atoms | 104 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |