| Experiment | |
|---|---|
Method _exptl.method | X-RAY DIFFRACTION |
Experimental protocol _diffrn_radiation.pdbx_diffrn_protocol | SINGLE WAVELENGTH |
Source type _diffrn_source.source | SYNCHROTRON |
Source details _diffrn_source.type | PHOTON FACTORY BEAMLINE AR-NE3A |
Synchrotron site _diffrn_source.pdbx_synchrotron_site | Photon Factory |
Beamline _diffrn_source.pdbx_synchrotron_beamline | AR-NE3A |
Temperature [K] _diffrn.ambient_temp | 100 |
Detector technology _diffrn_detector.detector | CCD |
Collection date _diffrn_detector.pdbx_collection_date | 2014-06-06 |
Detector _diffrn_detector.type | ADSC QUANTUM 315r |
Wavelength(s) [Å] _diffrn_source.pdbx_wavelength_list | 0.9204 |
| Software | |
Data reduction _software.classification | d*TREK |
Data scaling _software.classification | d*TREK (9.4SSI) |
Phasing _software.classification | PHASER |
Refinement _software.classification | PHENIX (1.17.1) |
| General information | |
Spacegroup name _symmetry.space_group_name_H-M | P 1 |
Unit cell parameters _cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma} | 24.296 24.852 28.249 93.85 106.02 103.21 |
Wavelength _diffrn_radiation_wavelength.wavelength | 0.92040 Å |
| Data quality metrics | Overall | InnerShell | OuterShell |
|---|---|---|---|
Low resolution limit [Å] _reflns.d_resolution_low _reflns_shell.d_res_low | 19.270 | 19.270 | 1.240 |
High resolution limit [Å] _reflns.d_resolution_high _reflns_shell.d_res_high | 1.200 | 2.580 | 1.200 |
Rmerge _reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs | 0.079 | 0.061 | 0.261 |
Rmeas _reflns.pdbx_Rrim_I_all | 0.079 | - | - |
| Rpim | - | - | - |
Total number of observations _reflns.pdbx_number_measured_all _reflns_shell.number_measured_all | 69661 | 6370 | 6621 |
Total number unique _reflns.number_obs _reflns_shell.number_unique_obs | 17973 | 1705 | 1766 |
<I/σ(I)> _reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs | 10.00 | 27.60 | 3.60 |
Completeness [%] _reflns.percent_possible_obs _reflns_shell.percent_possible_all | 93.8 | 89.1 | 92.3 |
Multiplicity _reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy | 3.9 | 3.6 | 3.8 |
| CC(1/2) | - | - | - |
| Refinement | |
|---|---|
PDB entry ID _entry.id | 7EDT |
Deposition date _pdbx_database_status.recvd_initial_deposition_date | 2021-03-17 |
Resolution _refine.ls_d_res_low _refine.ls_d_res_high | 19.3 - 1.200 Å |
Rwork/Rfree _refine.ls_R_factor_R_work _refine.ls_R_factor_R_free | 0.1439 / 0.1767 |
Structure solution method _refine.pdbx_method_to_determine_struct | MOLECULAR REPLACEMENT |
Starting model (for MR) _refine.pdbx_starting_model | RNA duplex constructed using Coot |