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Structure of RNase J2 wild type at room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K6W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.6 291 100mM tri-sodium citrate dihydrate pH 5.6, 20% PEG 4000, 20% Isopropanol, 40% Formamide
Crystal Properties Matthews coefficient Solvent content 1.99 38.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.304 α = 90 b = 133.38 β = 92.019 c = 117.751 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 278 IMAGE PLATE RIGAKU RAXIS IV 2022-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS IV 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.2 58.6 90.1 0.19 0.92 4.6 2.6 29972
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 0.6 0.48
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.2 58.6 29951 1392 89.671 0.207 0.2049 0.2079 0.2477 0.2471 38.488
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] 0.354 -0.024 0.568 -0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.212 r_dihedral_angle_3_deg 14.696 r_dihedral_angle_2_deg 10.107 r_lrange_it 9.404 r_lrange_other 9.404 r_dihedral_angle_1_deg 6.413 r_mcangle_it 4.222 r_mcangle_other 4.222 r_scangle_it 3.995 r_scangle_other 3.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.212 r_dihedral_angle_3_deg 14.696 r_dihedral_angle_2_deg 10.107 r_lrange_it 9.404 r_lrange_other 9.404 r_dihedral_angle_1_deg 6.413 r_mcangle_it 4.222 r_mcangle_other 4.222 r_scangle_it 3.995 r_scangle_other 3.995 r_scbond_it 2.456 r_scbond_other 2.456 r_mcbond_it 2.446 r_mcbond_other 2.442 r_angle_refined_deg 1.118 r_angle_other_deg 0.368 r_symmetry_nbd_refined 0.332 r_nbd_other 0.33 r_nbd_refined 0.207 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.147 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.04 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13034 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing