1K3D
Phosphoenolpyruvate carboxykinase in complex with ADP and AlF3
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AQ2 | PDB ID 1AQ2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 294 | ADP, Aluminum Nitrate, Magnesium Chloride, Sodium Fluoride, EDTA, ammonium acetate, sodium acetate buffer, dithiothreitol, PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.033 | α = 90 |
b = 95.844 | β = 95.59 |
c = 46.608 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 290 | DIFFRACTOMETER | WEISSENBERG | 1998-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-18B | 1.0 | Photon Factory | BL-18B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 40 | 96 | 0.071 | 3.8 | 35758 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
2 | 2.03 | 87.1 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ID 1AQ2 | 2 | 10 | 35230 | 35230 | 1787 | 0.198 | 0.198 | 0.196 | 0.266 | Random | 26 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_deg | 23.4 |
x_angle_deg | 1.4 |
x_improper_angle_deg | 1.09 |
x_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4127 |
Nucleic Acid Atoms | |
Solvent Atoms | 275 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |