2WVK
Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 apoprotein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2WVL | PDB ENTRY 2WVL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30-35% MPD WITH 600 MM ZNCL2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.6 | 65.7 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 113.456 | ¦Á = 90 |
b = 113.456 | ¦Â = 90 |
c = 195.982 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 41 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 | CCD | ADSC CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
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 | 2.97 | 45.2 | 99.4 | 0.11 | 19.5 | 18.9 | 26864 |
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 | 2.97 | 3.1 | 96.7 | 1.27 | 2.2 | 18.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 2WVL | 2.97 | 42.91 | 25502 | 1358 | 99.57 | 0.20122 | 0.19779 | 0.26636 | RANDOM | 71.327 |
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] | |
-0.17 | -0.17 | 0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.463 |
r_dihedral_angle_3_deg | 22.474 |
r_dihedral_angle_4_deg | 20.301 |
r_dihedral_angle_1_deg | 6.693 |
r_angle_refined_deg | 1.731 |
r_scbond_it | 1.175 |
r_scangle_it | 1.09 |
r_mcangle_it | 0.38 |
r_mcbond_it | 0.209 |
r_chiral_restr | 0.103 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6076 |
Nucleic Acid Atoms | |
Solvent Atoms | 74 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |