2OQF
Structure of a synthetic, non-natural analogue of RNase A: [N71K(Ade), D83A]RNase A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NUI | pdb entry 2NUI |
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.578 | α = 85.26 |
b = 50.534 | β = 74.31 |
c = 62.863 | γ = 82.7 |
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 | 77 | CCD | MARMOSAIC 300 mm CCD | 2006-08-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.3 | 50 | 19122 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 2NUI | 2.3 | 20 | 19122 | 17142 | 1958 | 97.56 | 0.23555 | 0.22927 | 0.23 | 0.2912 | 0.29 | RANDOM | 17.489 |
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] | |
1.72 | 0.02 | 1.34 | -1.78 | 1.1 | -0.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.479 |
r_dihedral_angle_3_deg | 13.99 |
r_dihedral_angle_4_deg | 10.674 |
r_dihedral_angle_1_deg | 6.058 |
r_angle_refined_deg | 1.214 |
r_scangle_it | 0.907 |
r_angle_other_deg | 0.752 |
r_scbond_it | 0.595 |
r_mcangle_it | 0.381 |
r_mcbond_it | 0.328 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3818 |
Nucleic Acid Atoms | |
Solvent Atoms | 91 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |