1KHT
Adenylate kinase from Methanococcus voltae
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 | 4.6 | 298 | PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.25 | 76.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 200.5 | α = 90 |
b = 200.5 | β = 90 |
c = 200.5 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 | MARRESEARCH | bent conical Si-mirror (Rh coating) | 1999-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 1.037 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 87.4 | 46286 | 39038 | 29.9 |
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 | 2.5 | 33.42 | 39038 | 39001 | 3917 | 84.2 | 0.2201 | 0.2201 | 0.22 | 0.253 | RANDOM |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.8 |
c_scangle_it | 2.24 |
c_mcangle_it | 2.21 |
c_scbond_it | 1.42 |
c_angle_deg | 1.3 |
c_mcbond_it | 1.22 |
c_improper_angle_d | 0.77 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4419 |
Nucleic Acid Atoms | |
Solvent Atoms | 179 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
AMoRE | phasing |
CNS | refinement |
XDS | data scaling |