3T7M
Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a triclinic closed form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3Q4S | PDB ENTRY 3Q4S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293.15 | 2.0M Ammonium Sulphate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.006 | α = 87.89 |
b = 47.081 | β = 78.88 |
c = 70.02 | γ = 76.65 |
Symmetry | |
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Space Group | P 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 | IMAGE PLATE | RIGAKU RAXIS IV | 2010-12-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.5418 |
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 | 1.8 | 45.81 | 92.9 | 0.077 | 12.3 | 3.8 | 49340 | 49335 | 19.5 |
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 | 1.8 | 1.9 | 87.9 | 0.524 | 2.3 | 3.4 | 6820 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | 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 | PDB ENTRY 3Q4S | 1.8 | 38.26 | 2 | 49335 | 46827 | 2508 | 92.87 | 0.19197 | 0.18923 | 0.24253 | RANDOM | 17.279 |
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] | |
0.63 | -1.18 | 0.66 | 0.63 | 0.26 | -0.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.568 |
r_dihedral_angle_3_deg | 13.681 |
r_dihedral_angle_4_deg | 12.854 |
r_dihedral_angle_1_deg | 6.352 |
r_angle_refined_deg | 1.552 |
r_angle_other_deg | 0.983 |
r_chiral_restr | 0.092 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4150 |
Nucleic Acid Atoms | |
Solvent Atoms | 509 |
Heterogen Atoms | 144 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |