1A3X
PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PG, MN2+ AND K+
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PKN | PDB ENTRY 1PKN |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6.5 | 28-33% (W/V) PEG 8000, 200 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE PH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 108.3 | α = 90 |
b = 106.4 | β = 110.8 |
c = 105.5 | 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 | 286 | IMAGE PLATE | RIGAKU RAXIS II | 1994-01-08 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R |
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 | 3 | 100 | 91 | 0.065 | 3.4 | 19294 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1PKN | 3 | 100 | 2 | 18430 | 1883 | 85 | 0.227 | 0.227 | 0.341 | RANDOM | 14 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 24.48 |
x_angle_deg | 1.736 |
x_improper_angle_d | 1.571 |
x_bond_d | 0.013 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7450 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |