8BRZ
Room-temperature structure of Pedobacter heparinus N-acetylglucosamine 2-epimerase at 52 MPa helium gas pressure in a sapphire capillary
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 295 | 12.6 mg/ml protein in 20 mM sodium phosphate buffer pH 7.5 were mixed (4+2 ul) with 0.1 M sodium cacodylate buffer pH 5.0, 0.35 M sodium acetate and 26% PEG 8000. Crystals grew at room temperature in 5-7 days. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.41 | α = 90 |
b = 94.08 | β = 102.63 |
c = 81.71 | 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 | 295 | PIXEL | DECTRIS PILATUS3 X CdTe 2M | 2020-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 0.477 | PETRA III, DESY | P11 |
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) | 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 | 1.7 | 41.28 | 96.35 | 0.2875 | 0.3072 | 0.1042 | 0.983 | 5.64 | 7.9 | 88642 | 17.71 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.7 | 1.761 | 82.55 | 1.751 | 1.892 | 0.6563 | 0.242 | 0.95 | 6 |
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 | 2GZ6 | 1.7 | 41.28 | 1.34 | 88072 | 1524 | 96.36 | 0.1579 | 0.1575 | 0.183 | 24.4 |
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 | 26.5443 |
f_angle_d | 0.6866 |
f_chiral_restr | 0.0403 |
f_bond_d | 0.0039 |
f_plane_restr | 0.0039 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6404 |
Nucleic Acid Atoms | |
Solvent Atoms | 474 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
Coot | model building |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | phasing |