5EFO
X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.63A.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4LWZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.949 | α = 67.54 |
b = 76.336 | β = 73.74 |
c = 89.694 | γ = 84.92 |
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 | PIXEL | PSI PILATUS 6M | 2015-05-15 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.97989 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.63 | 45.157 | 93.2 | 0.08 | 0.096 | 0.053 | 10.5 | 3.3 | 164109 | 164109 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.63 | 1.72 | 84.2 | 0.428 | 0.428 | 0.281 | 1.7 | 3.2 | 21679 |
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 | 4LWZ | 1.63 | 19.97 | 154258 | 8011 | 92.16 | 0.1652 | 0.163 | 0.2073 | RANDOM | 20.75 |
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] | |
-0.16 | -0.17 | 0.04 | -0.07 | -0.11 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 37.684 |
r_dihedral_angle_2_deg | 29.252 |
r_sphericity_bonded | 19.343 |
r_dihedral_angle_4_deg | 18.176 |
r_dihedral_angle_3_deg | 13.038 |
r_dihedral_angle_1_deg | 5.427 |
r_mcangle_it | 3.311 |
r_rigid_bond_restr | 3.09 |
r_scbond_it | 3.069 |
r_mcbond_it | 2.515 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11262 |
Nucleic Acid Atoms | |
Solvent Atoms | 1518 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |