5Y35
Phosphoglycerate mutase 1 complexed with a small molecule inhibitor KH1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4GPI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 289 | MES, pH 6.0, PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 63.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.836 | α = 90 |
b = 85.105 | β = 90 |
c = 103.046 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | ADSC QUANTUM 315r | 2014-05-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL18U1 | 0.97915 | SSRF | BL18U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.99 | 50 | 95.3 | 0.171 | 0.173 | 0.074 | 6.1 | 6.7 | 47888 | 24.84 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.99 | 2.06 | 100 | 0.974 | 0.384 | 0.738 | 7.3 |
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 | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4GPI | 1.994 | 43.751 | 1.33 | 47158 | 2415 | 93.65 | 0.2177 | 0.2162 | 0.2439 | 34.04 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
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 |
f_dihedral_angle_d | 14.776 |
f_angle_d | 1.202 |
f_chiral_restr | 0.049 |
f_bond_d | 0.009 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3782 |
Nucleic Acid Atoms | |
Solvent Atoms | 302 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
HKL-2000 | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |