1S3G
Crystal structure of adenylate kinase from Bacillus globisporus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1P3J | PDB ENTRY 1P3J |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | small-scale batch method | 7 | 293 | ammonium sulfate, PEG 1000, sodium azide, pH 7.0, small-scale batch method, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 47.93 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 65.288 | ¦Á = 90 |
b = 65.288 | ¦Â = 90 |
c = 94.378 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | MAR CCD 165 mm | 2003-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 1.1271 | APS | 14-ID-B |
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 | 2.25 | 50 | 99.2 | 0.057 | 24.6 | 5.2 | 21054 | 32.6 |
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) | |||||||||||
2.25 | 2.33 | 99.4 | 0.593 | 2.5 | 4.6 | 1112 |
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 1P3J | 2.25 | 27.49 | 19702 | 19702 | 1739 | 92.5 | 0.223 | 0.223 | 0.288 | RANDOM | 51.5 |
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] | |
-1.65 | 1.98 | -1.65 | 3.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 20.8 |
c_scangle_it | 6.28 |
c_scbond_it | 5.15 |
c_mcangle_it | 2.55 |
c_mcbond_it | 1.61 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.82 |
c_bond_d | 0.017 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1684 |
Nucleic Acid Atoms | |
Solvent Atoms | 109 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SOMORE | phasing |