5CCO
Staphylococcus bacteriophage 80alpha dUTPase with dUMP.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ZEZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 294 | 60% ethanol, 0.1 M NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.87 | 57.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87 | α = 90 |
b = 87 | β = 90 |
c = 87 | γ = 90 |
Symmetry | |
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Space Group | P 21 3 |
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 QUANTUM 315r | 2010-07-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.98 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.33 | 61.52 | 99.9 | 0.031 | 16.2 | 11 | 9645 |
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 | 2.33 | 2.46 | 100 | 0.1 | 6.2 | 10.6 |
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 | 3zez | 2.33 | 61.52 | 9080 | 541 | 99.74 | 0.20322 | 0.20099 | 0.24437 | RANDOM | 38.035 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.704 |
r_dihedral_angle_3_deg | 16.871 |
r_dihedral_angle_4_deg | 15.726 |
r_dihedral_angle_1_deg | 7.03 |
r_long_range_B_other | 6.499 |
r_long_range_B_refined | 6.493 |
r_scangle_other | 4.905 |
r_mcangle_it | 3.754 |
r_mcangle_other | 3.753 |
r_scbond_it | 3.081 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1289 |
Nucleic Acid Atoms | |
Solvent Atoms | 66 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
MOLREP | phasing |
MOSFLM | data reduction |