1NBS
Crystal structure of the specificity domain of Ribonuclease P RNA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 303 | isopropanol, strontium chloride, magnesium chloride, spermine, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.31 | 62.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.5 | α = 90 |
b = 145.3 | β = 90 |
c = 144.6 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | MARRESEARCH | mirrors | 2002-04-23 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 5ID-B | 0.9475,0.9293 | APS | 5ID-B |
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 | 3.15 | 33 | 98.2 | 0.076 | 7.8 | 10.1 | 23276 | 23276 | 66.3 |
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) | |||||||||||
3.15 | 3.24 | 80.9 | 0.272 | 2.7 | 2.9 | 1345 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 3.15 | 33 | 22853 | 21680 | 1173 | 98.18 | 0.28179 | 0.28179 | 0.28043 | 0.30736 | RANDOM | 94.249 |
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] | |
4.45 | -0.56 | -3.9 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 2.417 |
r_scbond_it | 1.487 |
r_angle_refined_deg | 1.291 |
r_symmetry_vdw_refined | 0.35 |
r_nbd_refined | 0.281 |
r_symmetry_hbond_refined | 0.174 |
r_xyhbond_nbd_refined | 0.161 |
r_chiral_restr | 0.139 |
r_gen_planes_refined | 0.017 |
r_bond_refined_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 5802 |
Solvent Atoms | |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
SHARP | phasing |
CNS | refinement |
XDS | data scaling |
XDS | data reduction |
CCP4 | data scaling |