3OPY
Crystal structure of Pichia pastoris phosphofructokinase in the T-state
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 4.6 | 292 | 1 microliter of protein + 1 microliter of reservoir using streak seading, protein: 1mg/mL PFK, 10mM imidazol, 5mM mercaptoethanol, 10% glycerol, 10mM ATP, pH 7.0; reservoir: 0.7M ammonia sulfate, 0.1M sodium citrate pH 4.6, VAPOR DIFFUSION, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.47 | 64.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 161.658 | α = 90 |
b = 188.303 | β = 92.85 |
c = 231.56 | 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 | RAYONIX MX225HE | Double crystal monochromator with 2 sets of mirrors | 2009-03-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.918 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.05 | 29.8 | 53.2 | 97.5 | 262877 | 1 | 1 | 75.78 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 3.05 | 29.8 | 617625 | 255838 | 12864 | 0.247 | 0.2019 | 0.2003 | 0.2318 | RANDOM | 68.17 |
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] | |
-13.4997 | -1.0224 | 9.7517 | 3.748 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 22.51 |
t_omega_torsion | 2.58 |
t_angle_deg | 1.24 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 64576 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 449 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
MOLREP | phasing |
BUSTER | refinement |
XDS | data reduction |
XDS | data scaling |