3T7N
Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a monoclinic 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 | 8.5 | 293.15 | 20% PEG 3350, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.02 | α = 90 |
b = 80.72 | β = 100.92 |
c = 69.85 | 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV | 2011-01-19 | 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 | 1.98 | 30.43 | 97.3 | 0.074 | 10.7 | 3.3 | 34716 | 34694 | 25.2 |
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 | 1.98 | 2.09 | 95.3 | 0.497 | 2.1 | 3.2 | 4921 |
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 | 1.98 | 29.16 | 2 | 34694 | 32947 | 1745 | 96.99 | 0.20632 | 0.20326 | 0.26546 | RANDOM | 34.106 |
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] | |
-1.43 | -2.48 | 2.61 | -2.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.521 |
r_dihedral_angle_4_deg | 18.51 |
r_dihedral_angle_3_deg | 15 |
r_dihedral_angle_1_deg | 6.395 |
r_scangle_it | 2.772 |
r_scbond_it | 1.947 |
r_angle_refined_deg | 1.487 |
r_mcangle_it | 1.234 |
r_angle_other_deg | 0.974 |
r_mcbond_it | 0.701 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4027 |
Nucleic Acid Atoms | |
Solvent Atoms | 286 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |