4ZXL
CpOGA D298N in complex with Drosophila HCF -derived Thr-O-GlcNAc peptide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 295.15 | CpOGA D298N was concentrated to 35 mg/ml in 25 mM Tris/HCl (pH 8.0) and crystallized from 0.175 M CdSO4 and 0.6 M sodium acetate pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.6 | 73.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 118.56 | α = 90 |
b = 118.56 | β = 90 |
c = 148.441 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | PIXEL | PSI PILATUS 6M | 2015-02-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.8729 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.6 | 34.9 | 99.4 | 0.152 | 7.3 | 3.3 | 36087 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.72 | 99 | 0.862 | 3.3 | 4368 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 2yds | 2.6 | 34.9 | 35353 | 729 | 99.26 | 0.17155 | 0.17051 | 0.2201 | RANDOM | 42.751 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 45.638 |
r_dihedral_angle_2_deg | 37.794 |
r_sphericity_bonded | 28.239 |
r_dihedral_angle_3_deg | 13.842 |
r_dihedral_angle_4_deg | 13.452 |
r_dihedral_angle_1_deg | 5.12 |
r_rigid_bond_restr | 1.467 |
r_angle_refined_deg | 1.007 |
r_chiral_restr | 0.069 |
r_bond_refined_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4601 |
Nucleic Acid Atoms | |
Solvent Atoms | 75 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |