4L3Q
Crystal structure of glucokinase-activator complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 57.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.512 | α = 90 |
b = 79.512 | β = 90 |
c = 321.131 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 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 | 98 | IMAGE PLATE | MAR scanner 345 mm plate | Mirrors | 2004-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 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 | 2.7 | 50 | 97.4 | 0.042 | 32.3 | 17490 | 17045 | 1 | 1 |
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) | |||||||||||
1 | 2.7 | 2.8 | 99.8 | 0.155 | 9.3 | 4.1 | 1678 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 1V4S | 2.7 | 39.84 | 15665 | 1769 | 99.59 | 0.2591 | 0.25415 | 0.30377 | RANDOM | 52.461 |
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] | |
-0.1 | -0.05 | -0.1 | 0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.872 |
r_scangle_it | 3.439 |
r_scbond_it | 1.946 |
r_mcangle_it | 1.683 |
r_angle_refined_deg | 1.511 |
r_mcbond_it | 0.89 |
r_symmetry_hbond_refined | 0.281 |
r_nbd_refined | 0.237 |
r_symmetry_vdw_refined | 0.236 |
r_xyhbond_nbd_refined | 0.143 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3499 |
Nucleic Acid Atoms | |
Solvent Atoms | 6 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
CNX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNX | phasing |