1KI9
Adenylate kinase from Methanococcus thermolithotrophicus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NKS | PDB entry 1NKS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | PEG 6000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 55.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.5 | α = 90 |
b = 128.5 | β = 90 |
c = 88.5 | γ = 90 |
Symmetry | |
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Space Group | P 4 21 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 | IMAGE PLATE | RIGAKU RAXIS IV | confocal | 1999-02-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 2.5 | 50 | 94.7 | 0.068 | 27043 | 25623 | 32.7 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1NKS | 2.76 | 30.78 | 18370 | 18370 | 1812 | 94 | 0.2041 | 0.2041 | 0.204 | 0.287 | RANDOM | 43 |
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] | |
2.83 | 2.83 | -5.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 20.7 |
c_scangle_it | 4.88 |
c_mcangle_it | 3.79 |
c_scbond_it | 3.42 |
c_mcbond_it | 2.35 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.76 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4498 |
Nucleic Acid Atoms | |
Solvent Atoms | 160 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Crystal | data collection |
d*TREK | data reduction |
AMoRE | phasing |
CNS | refinement |
CrystalClear | data reduction |
d*TREK | data scaling |