3H86
Crystal structure of adenylate kinase from Methanococcus maripaludis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.7 | 273 | 3.4 M ammonium chloride, 0.1 M sodium acetate, 3% ethylene glycol (v/v)., pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.84 | α = 90 |
b = 102.84 | β = 90 |
c = 228.72 | γ = 120 |
Symmetry | |
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Space Group | H 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 | 103 | IMAGE PLATE | RIGAKU RAXIS IV | Rigaku Osmic Mirrors | 2008-08-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.54 |
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 | 29.69 | 99.9 | 0.082 | 9.6 | 2.44 | 31194 | 31158 | 3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.5 | 2.59 | 100 | 0.33 | 2.3 | 2.4 | 3109 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1KHT | 2.5 | 19.7 | 31158 | 27970 | 3138 | 99.86 | 0.18821 | 0.18268 | 0.23911 | RANDOM | 59.467 |
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] | |
9.05 | 9.05 | -18.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_2_deg | 32.944 |
f_dihedral_angle_4_deg | 20.369 |
f_dihedral_angle_3_deg | 20.275 |
f_dihedral_angle_1_deg | 7.119 |
f_scangle_it | 4.547 |
f_scbond_it | 3.002 |
f_angle_refined_deg | 2.151 |
f_mcangle_it | 1.995 |
f_mcbond_it | 1.12 |
f_chiral_restr | 0.124 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5848 |
Nucleic Acid Atoms | |
Solvent Atoms | 43 |
Heterogen Atoms | 228 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
PHENIX | refinement |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |