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Crystal structure of the ribonuclease core of R3B2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291.15 100 mM Hepes/NaOH pH 7.0, 200 mM L-proline and 12% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.91 α = 90 b = 80.759 β = 90 c = 83.783 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M-F 2018-09-07 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA 2 SYNCHROTRON SLS BEAMLINE X10SA 2.0 SLS X10SA
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 1.65 37.95 99.8 0.044 0.048 0.018 0.999 21.8 12.4 62534
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 96.9 0.594 9.1
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SIRAS FREE R-VALUE 1.65 37.953 62453 1917 99.725 0.163 0.1621 0.1824 0.1634 40.541
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] 1.397 -3.376 1.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.685 r_dihedral_angle_4_deg 26.052 r_dihedral_angle_3_deg 13.614 r_dihedral_angle_1_deg 5.868 r_lrange_it 4.476 r_lrange_other 4.357 r_scangle_other 3.176 r_scangle_it 3.175 r_mcangle_it 3.044 r_mcangle_other 3.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.685 r_dihedral_angle_4_deg 26.052 r_dihedral_angle_3_deg 13.614 r_dihedral_angle_1_deg 5.868 r_lrange_it 4.476 r_lrange_other 4.357 r_scangle_other 3.176 r_scangle_it 3.175 r_mcangle_it 3.044 r_mcangle_other 3.044 r_scbond_it 2.537 r_scbond_other 2.532 r_mcbond_it 2.158 r_mcbond_other 2.151 r_angle_other_deg 1.297 r_angle_refined_deg 1.283 r_rigid_bond_restr 1.22 r_nbd_refined 0.197 r_nbd_other 0.187 r_symmetry_nbd_other 0.17 r_symmetry_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.13 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.01 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2282 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data reduction AutoSol phasing DIALS data processing Aimless data scaling