6DVK
Computationally designed mini tetraloop-tetraloop receptor by the RNAMake program - construct 6 (miniTTR 6)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 298 | 40 mM sodium cacodylate (pH 5.5), 20 mM MgCl2, 2 mM cobalt hexammine, and 40% 2-methyl-2,4-pentanediol (MPD) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.04 | 39.82 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 233.372 | α = 90 |
b = 25.358 | β = 99.74 |
c = 42.861 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 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 | CMOS | RDI CMOS_8M | 2016-09-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 1.58954 | ALS | 4.2.2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.55 | 115 | 97.6 | 0.146 | 0.176 | 0.984 | 6.44 | 3.01 | 8270 | 39.918 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.55 | 2.62 | 94.2 | 0.903 | 1.127 | 0.339 | 1.03 | 2.604 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.55 | 115 | 7897 | 377 | 97.72 | 0.2332 | 0.2315 | 0.2685 | RANDOM | 38.435 |
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 | -0.09 | -0.67 | -0.96 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_angle_other_deg | 1.616 |
r_angle_refined_deg | 1.367 |
r_chiral_restr | 0.095 |
r_gen_planes_refined | 0.008 |
r_bond_refined_d | 0.006 |
r_bond_other_d | 0.004 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 2008 |
Solvent Atoms | 2 |
Heterogen Atoms | 15 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |