3D8Z
RNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2G8Q | PDB entry 2G8Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 289 | PEG 4000, SODIUM CITRATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.102 | α = 90 |
b = 32.678 | β = 90.51 |
c = 72.562 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | CCD | ADSC QUANTUM 4 | 2006-11-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.6 | 0.92 | SRS | PX9.6 |
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 | 1.98 | 30 | 98.9 | 0.091 | 8.7 | 2.9 | 16850 | 16481 | -3 | 21 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.98 | 2.03 | 100 | 0.435 | 2.8 | 2.9 | 852 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 2G8Q | 1.98 | 28.6 | 16850 | 15649 | 832 | 97.82 | 0.19178 | 0.18929 | 0.24022 | RANDOM | 18.096 |
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] | |
-0.14 | -0.1 | 0.29 | -0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.959 |
r_dihedral_angle_3_deg | 13.308 |
r_dihedral_angle_4_deg | 13.076 |
r_dihedral_angle_1_deg | 6.39 |
r_scangle_it | 2.5 |
r_scbond_it | 1.602 |
r_angle_refined_deg | 1.58 |
r_mcangle_it | 0.87 |
r_mcbond_it | 0.526 |
r_nbtor_refined | 0.291 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1902 |
Nucleic Acid Atoms | |
Solvent Atoms | 166 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |