2VFZ
CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN COMPLEX WITH UDP-2F-GALACTOSE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 10% PEG 6000, 0.1M TRIS-HCL, PH 8.0 AND 12-20% MPD |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 59 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 44.735 | ¦Á = 83.34 |
b = 64.759 | ¦Â = 83.95 |
c = 66.468 | ¦Ã = 70.14 |
Symmetry | |
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Space Group | P 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 | MIRRORS | 2005-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX14.1 | 0.977, 1.48 | SRS | PX14.1 |
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 | 2.4 | 50 | 89.9 | 0.05 | 11.5 | 4 | 27634 | 24.7 |
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 | 2.4 | 2.49 | 67.2 | 0.13 | 4.44 | 1.9 |
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 | NONE | 2.4 | 25.06 | 23881 | 1157 | 87.9 | 0.178 | 0.178 | 0.233 | RANDOM | 29 |
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] | |
-3.36 | -3.29 | 2.4 | 3.95 | -14.76 | -0.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.9 |
c_improper_angle_d | 4.17 |
c_scangle_it | 2.55 |
c_mcangle_it | 1.86 |
c_scbond_it | 1.76 |
c_angle_deg | 1.5 |
c_mcbond_it | 1.16 |
c_bond_d | 0.013 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4654 |
Nucleic Acid Atoms | |
Solvent Atoms | 497 |
Heterogen Atoms | 74 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |