2BQ1
Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PEM | PDB ENTRY 1PEM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 1:1 MIX OF PROTEIN SOLUTION (8 MG/ML R1E, 4 MG/ML R2F, 1.5 MM DGTP, 1.5 MM ADP, 1.5 MM MGCL2 AND 1.5 MM HYDROXYUREA) AND RESERVOIR SOLUTION CONSISTING OF 100 MM NAHEPES PH 7.5 AND 1.8 M SODIUM FORMATE. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.79 | 66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 270.372 | α = 90 |
b = 270.372 | β = 90 |
c = 270.372 | γ = 90 |
Symmetry | |
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Space Group | P 41 3 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 | CCD | ADSC CCD | 2004-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
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 | 4 | 40 | 99.8 | 0.15 | 13.5 | 15.1 | 29196 | 1 |
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 | 4 | 4.07 | 98.8 | 0.39 | 4 | 7.2 |
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 1PEM | 3.99 | 182.57 | 27672 | 1484 | 99.7 | 0.265 | 0.262 | 0.31 | RANDOM | 65.31 |
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_1_deg | 5.546 |
r_scangle_it | 1.07 |
r_angle_refined_deg | 1.036 |
r_mcangle_it | 0.724 |
r_scbond_it | 0.574 |
r_mcbond_it | 0.393 |
r_nbd_refined | 0.216 |
r_symmetry_vdw_refined | 0.187 |
r_symmetry_hbond_refined | 0.176 |
r_xyhbond_nbd_refined | 0.161 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15452 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 68 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
BEAST | phasing |