RNase A-Uridine 5'-Hexaphosphate (RNaseA.p6U)
X-RAY DIFFRACTION - SOLUTION SCATTERING
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1AFU | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 295 | 25% PEG4000, 20 mM citrate, pH 6, crystal soaked in 50 mM ligand, 30% PEG4000, 25% glycerol, 20 mM citrate |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.16 | 43.06 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 100.069 | α = 90 |
| b = 32.527 | β = 90.48 |
| c = 72.785 | 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 | CCD | APEX II CCD | | 2022-10-23 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | BRUKER AXS MICROSTAR-H | 1.544178 | | |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.79 | 30.93 | 99.29 | | 0.05 | | | | | 3.13 | 17.13 | | 22299 | | | 17.55 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.79 | 1.86 | | | 0.05 | | | | | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.79 | 30.93 | | 1.34 | | 22299 | 1137 | 99.29 | | 0.1808 | 0.1782 | 0.18 | 0.2309 | 0.23 | | 25.5 |
| 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] |
|---|
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 34.3247 |
| f_angle_d | 1.3843 |
| f_chiral_restr | 0.0616 |
| f_bond_d | 0.0119 |
| f_plane_restr | 0.0099 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1894 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 248 |
| Heterogen Atoms | 123 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PHENIX | refinement |
| SAINT | data reduction |
| SADABS | data scaling |
| PHENIX | phasing |
