4FXF
Structure of M2 pyruvate kinase in complex with phenylalanine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BJT | PDB entry 3BJT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 290 | 10-16% PEG 8000, 100 mM sodium Cacodylate, 50 mM MgCl2, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.21 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 81.6 | ¦Á = 90 |
b = 139.35 | ¦Â = 90.52 |
c = 111.28 | ¦Ã = 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 | PIXEL | PSI PILATUS 6M | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 1.0 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.55 | 66.09 | 98.2 | 0.085 | 0.053 | 15.6 | 6.9 | 79477 | 2.55 | 2.55 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.55 | 2.62 | 93.6 | 0.633 | 0.757 | 2.6 | 6.5 | 36105 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3BJT | 2.55 | 51.67 | 75250 | 3978 | 100 | 0.21453 | 0.21243 | 0.25376 | RANDOM | 49.578 |
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] | |
-0.16 | -0.08 | 0.04 | 0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.104 |
r_dihedral_angle_3_deg | 13.676 |
r_dihedral_angle_4_deg | 13.267 |
r_dihedral_angle_1_deg | 4.122 |
r_angle_refined_deg | 0.878 |
r_scangle_it | 0.787 |
r_mcangle_it | 0.437 |
r_scbond_it | 0.431 |
r_mcbond_it | 0.237 |
r_chiral_restr | 0.053 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15352 |
Nucleic Acid Atoms | |
Solvent Atoms | 428 |
Heterogen Atoms | 176 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |