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Crystal Structure of Thermus thermophilus KhpB/EloR complexed with RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES (pH 7.5), 0.2M ammonium sulfate, 25% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.261 α = 97.34 b = 46.058 β = 92.53 c = 56.885 γ = 112.693
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 RAYONIX MX225HE 2017-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 2.65 36.99 97.7 0.09 0.103 0.031 0.999 30.1 8.3 10994 62.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.75 97.3 0.2 0.231 0.088 0.902 7.5
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 2.65 32.382 9273 492 97.724 0.207 0.2036 0.207 0.2653 0.265 38.027
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] -0.036 0.016 0.088 0.055 0.088 -0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.129 r_dihedral_angle_6_deg 15.63 r_lrange_it 8.763 r_lrange_other 8.763 r_scangle_it 6.311 r_scangle_other 6.309 r_dihedral_angle_1_deg 5.686 r_dihedral_angle_2_deg 5.308 r_mcangle_it 5.061 r_mcangle_other 5.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.129 r_dihedral_angle_6_deg 15.63 r_lrange_it 8.763 r_lrange_other 8.763 r_scangle_it 6.311 r_scangle_other 6.309 r_dihedral_angle_1_deg 5.686 r_dihedral_angle_2_deg 5.308 r_mcangle_it 5.061 r_mcangle_other 5.06 r_scbond_it 4.169 r_scbond_other 4.167 r_mcbond_it 3.291 r_mcbond_other 3.289 r_angle_refined_deg 1.172 r_angle_other_deg 0.384 r_symmetry_xyhbond_nbd_refined 0.268 r_symmetry_nbd_refined 0.264 r_nbd_refined 0.228 r_nbd_other 0.2 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.169 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.054 r_dihedral_angle_other_2_deg 0.028 r_bond_refined_d 0.006 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 2301 Nucleic Acid Atoms 140 Solvent Atoms 5 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling PHASER phasing