☰ Navigation Tabs
Sarcin-ricin loop with guanosine dithiophosphate residue.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S7C PDB ID: 3S7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Crystallization set-ups were made by mixing 4 uL of 350 uM RNA solution [1 mM
Na 2 EDTA (pH 8.0) and 10 mM Tris-HCl (pH 8.0)] with 2 uL of a crystallization buffer composed of 3.0 M ammonium sulfate,
10 mM magnesium chloride, 10 mM manganese chloride, and 50 mM potassium 3-(N-morpholino) propanesulfonic acid (MOPS), pH 7.0 at 18 C.
Crystal Properties Matthews coefficient Solvent content 1.91 35.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.581 α = 90 b = 29.581 β = 90 c = 76.653 γ = 90
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 MARMOSAIC 300 mm CCD 2018-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (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 1.25 30 99.5 0.065 0.028 40.06 6 18152
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.29 99.3 0.51 0.239 2.76 5.3
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID: 3S7C 1.25 27.6 17225 901 99.47 0.1122 0.1103 0.1157 0.1478 0.147 RANDOM 15.641
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] -1.63 -1.63 3.26
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 6.432 r_angle_refined_deg 1.745 r_angle_other_deg 1.67 r_chiral_restr 0.109 r_gen_planes_refined 0.028 r_bond_refined_d 0.011 r_gen_planes_other 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 579 Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing