5CI1
Ribonucleotide reductase Y122 2,3-F2Y variant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ALX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8 | 293 | 1.1 M (NH4)2SO4, 0.9-1.2 M KCl, and 0.1 M Tris pH 8.0; 1:1 protein to precipitant; crystals grow over 1-3 days |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.85 | 61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.589 | α = 90 |
b = 90.589 | β = 90 |
c = 209.468 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 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 | PIXEL | DECTRIS PILATUS 6M-F | 2012-07-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97950 | APS | 24-ID-C |
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 | 1.95 | 50 | 97.3 | 0.072 | 10.72 | 5.1 | 36925 |
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 | 1.95 | 1.98 | 98.9 | 0.786 | 2.02 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | 2ALX | 1.95 | 37.999 | 1.35 | 36925 | 1828 | 97.35 | 0.1558 | 0.1543 | 0.1833 | Random |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.964 |
f_angle_d | 1.327 |
f_chiral_restr | 0.057 |
f_bond_d | 0.014 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2856 |
Nucleic Acid Atoms | |
Solvent Atoms | 209 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data scaling |
PHASER | phasing |
HKL-2000 | data reduction |