3ME3
Activator-Bound Structure of Human Pyruvate Kinase M2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GQY | isomorphous pdb entry 3GQY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 291 | 25% w/v PEG-3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, 0.005M activator (from 0.1M stock solution in DMSO)., pH 6.5, vapor diffusion, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 49.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.882 | α = 90 |
b = 152.564 | β = 103.17 |
c = 93.036 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | RIGAKU SATURN A200 | 2010-03-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 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 | 1.95 | 40 | 99.8 | 0.08 | 10.7 | 3.6 | 158866 |
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) | |||||||||||
1 | 1.95 | 1.98 | 97.4 | 0.857 | 3 | 7719 |
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 | THROUGHOUT | isomorphous pdb entry 3GQY | 1.95 | 26.714 | 158798 | 1914 | 99.682 | 0.219 | 0.219 | 0.262 | thin shells (sftools) | 23.419 |
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] | |
-0.709 | -1.136 | 0.028 | 0.163 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.075 |
r_dihedral_angle_4_deg | 15.671 |
r_dihedral_angle_3_deg | 13.272 |
r_dihedral_angle_1_deg | 5.71 |
r_scangle_it | 3.245 |
r_scbond_it | 2.045 |
r_angle_refined_deg | 1.425 |
r_mcangle_it | 1.284 |
r_angle_other_deg | 0.906 |
r_mcbond_it | 0.723 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15143 |
Nucleic Acid Atoms | |
Solvent Atoms | 675 |
Heterogen Atoms | 202 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |