2C5A
GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2C54 | PDB ENTRY 2C54 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 100 MM BIS-TRIS PH 6.0, 2.2M AMMONIUM SULPHATE, SITTING DROP, VAPOUR DIFFUSION. CRYOPROTECTED 6 M SODIUM FORMATE. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.16 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 62.497 | ¦Á = 90 |
b = 83.273 | ¦Â = 98.89 |
c = 66.12 | ¦Ã = 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 | CCD | ADSC CCD | 2005-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 1.4 | 23.12 | 96.7 | 0.05 | 17.9 | 3.6 | 126826 | 11 |
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 | 1.4 | 1.48 | 95.4 | 0.23 | 5.5 | 3.5 |
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 2C54 | 1.4 | 21.61 | 126798 | 6337 | 96.5 | 0.105 | 0.103 | 0.14 | RANDOM | 9.78 |
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] | |
-0.262 | -0.05 | 0.589 | -0.342 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.509 |
r_dihedral_angle_4_deg | 21.328 |
r_dihedral_angle_3_deg | 12.532 |
r_dihedral_angle_1_deg | 6.407 |
r_scangle_it | 4.774 |
r_scbond_it | 3.673 |
r_mcangle_it | 2.518 |
r_mcbond_it | 2.188 |
r_angle_refined_deg | 1.921 |
r_angle_other_deg | 1.086 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5786 |
Nucleic Acid Atoms | |
Solvent Atoms | 1018 |
Heterogen Atoms | 231 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |