3Q1R
Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and in the presence of 5' leader
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 303 | 1.8M LiSO4, 0.5M sodium cacolydate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.95 | 75.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 169.92 | α = 90 |
b = 169.92 | β = 90 |
c = 185.53 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX-225 | MIRRORS | 2010-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 4.2 | 30 | 76.4 | 0.081 | 0.099 | 10.7 | 5.7 | 17674 | 153.42 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
4.2 | 4.39 | 7.8 | 0.463 | 0.577 | 2.4 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MIRAS | THROUGHOUT | 2A2E, 2A64, 1NZ0, 1EHZ | 4.21 | 29.63 | 17651 | 913 | 0.259 | 0.258 | 0.267 | RANDOM | 80.04 |
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] | |
-21.3244 | -21.3244 | 42.6489 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_angle_deg | 1.23 |
t_bond_d | 0.007 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 973 |
Nucleic Acid Atoms | 9208 |
Solvent Atoms | |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
MD2 | data collection |
BUSTER | refinement |
XDS | data reduction |
SCALA | data scaling |