3RMW
Crystal Structure of Human Glycogenin-1 (GYG1) T83M mutant complexed with manganese and UDP-glucose
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 | 293.15 | 25% PEG smears (PEG 6k, 8k, 10k), 0.2M MgCl2, 10% glycerol, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.89 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.65 | α = 90 |
b = 100.61 | β = 90 |
c = 49.1 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 2010-10-26 | 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 | 1.93 | 29.85 | 100 | 0.097 | 10.7 | 4.5 | 21806 | 21806 | 25.5 |
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 | 1.93 | 2.03 | 100 | 0.728 | 2 | 4.4 | 3129 |
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 | 1.93 | 28.86 | 2 | 21806 | 20690 | 1116 | 99.98 | 0.18674 | 0.1841 | 0.23735 | RANDOM | 22.627 |
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] | |
-0.61 | -0.54 | 1.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.602 |
r_dihedral_angle_4_deg | 16.575 |
r_dihedral_angle_3_deg | 13.224 |
r_dihedral_angle_1_deg | 6.947 |
r_sphericity_free | 5.476 |
r_sphericity_bonded | 5.33 |
r_scangle_it | 3.478 |
r_scbond_it | 2.292 |
r_mcangle_it | 1.464 |
r_angle_refined_deg | 1.404 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1954 |
Nucleic Acid Atoms | |
Solvent Atoms | 189 |
Heterogen Atoms | 86 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |