8SSG
Minimal protein-only/RNA-free Ribonuclease P from Hydrogenobacter thermophilus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 277.15 | 1.0 M Sodium Malonate, pH 5.0, 0.1 M Sodium Acetate trihydrate, pH 4.5, 2% (w/v) polyethylene glycol 20,000 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.88 | 57.17 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 102.317 | α = 90 |
b = 113.764 | β = 90 |
c = 155.306 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2020-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.03317 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 3.2 | 29.84 | 99.9 | 0.116 | 0.137 | 0.071 | 0.999 | 12.1 | 6.8 | 30570 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 3.2 | 3.37 | 1.799 | 2.104 | 1.082 | 0.43 | 7.2 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7f3e | 3.2 | 29.739 | 30535 | 1524 | 99.81 | 0.2 | 0.1977 | 0.2485 | 120.427 |
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] | |
-2.565 | 2.988 | -0.423 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_lrange_it | 27.129 |
r_scangle_it | 21.133 |
r_dihedral_angle_3_deg | 18.443 |
r_dihedral_angle_2_deg | 18.126 |
r_mcangle_it | 17.283 |
r_dihedral_angle_6_deg | 15.617 |
r_scbond_it | 13.845 |
r_mcbond_it | 11.399 |
r_dihedral_angle_1_deg | 4.761 |
r_angle_refined_deg | 2.076 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 10010 |
Nucleic Acid Atoms | |
Solvent Atoms | 30 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PHASER | phasing |
DIALS | data processing |
DIALS | data reduction |