4ZA0
Structure of Human Enolase 2 in complex with Phosphonoacetohydroxamate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 100 mM Bis-Tris, pH 6.5, 200 mM ammonium acetate, 18-22% w/v PEG3350, overnight crystal soak in 2 mM PhaH, 100 mM Bis-Tris, 200 mM ammonium acetate, 32% w/v PEG3350, pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.79 | α = 90 |
b = 108.671 | β = 90 |
c = 112.21 | 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 | 2014-10-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11587 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 2.31 | 67.79 | 100 | 0.22 | 0.065 | 0.993 | 10.9 | 12.4 | 37271 | 37271 | 18.35 |
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 | 2.31 | 2.39 | 100 | 0.84 | 0.257 | 0.844 | 3.1 | 11.4 | 3599 |
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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 3UCC chain A | 2.31 | 58.023 | 1.34 | 37211 | 1942 | 99.94 | 0.166 | 0.1639 | 0.2036 | Random selection | 20.0036 |
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 | 13.291 |
f_angle_d | 0.638 |
f_chiral_restr | 0.023 |
f_bond_d | 0.009 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6629 |
Nucleic Acid Atoms | |
Solvent Atoms | 488 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
PHENIX | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |