2Y4L
MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH Manganese and GDP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BO7 | PDB ENTRY 2BO7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5 | 4% V/V ETHYLENE GLYCOL, 0.1 M BIS-TRIS PROPANE PH 5.5, 0.2 MNCL2, 0.4 M SODIUM MALONATE. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.61 | 78.1 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 149.756 | ¦Á = 90 |
b = 149.756 | ¦Â = 90 |
c = 154.71 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 32 2 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 | CCD | ADSC CCD | 2009-09-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 |
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 | 2.8 | 50 | 100 | 0.08 | 22.3 | 10.9 | 47314 | 2 | 54.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.8 | 2.9 | 100 | 0.59 | 3.9 | 10.7 |
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 | PDB ENTRY 2BO7 | 2.8 | 129.69 | 47314 | 2530 | 99.85 | 0.1893 | 0.18762 | 0.22041 | RANDOM | 48.073 |
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] | |
-0.49 | -0.25 | -0.49 | 0.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.28 |
r_dihedral_angle_3_deg | 18.61 |
r_dihedral_angle_4_deg | 16.612 |
r_dihedral_angle_1_deg | 6.207 |
r_scangle_it | 4.213 |
r_scbond_it | 2.471 |
r_mcangle_it | 1.676 |
r_angle_refined_deg | 1.67 |
r_mcbond_it | 0.837 |
r_chiral_restr | 0.112 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6179 |
Nucleic Acid Atoms | |
Solvent Atoms | 101 |
Heterogen Atoms | 108 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |