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Crystal structure of rRNA (uracil-C5)-methyltransferase from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-O58994-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 293 0.1 M HEPES sodium pH 7.5, 2% (v/v) PEG 400, 2.0 M ammounium sulfate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.89 α = 90 b = 96.61 β = 90 c = 122.4 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 IMAGE PLATE RIGAKU RAXIS IV++ Vari Max 2023-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 3.2 96.61 100 0.224 0.239 0.083 0.986 8.3 8 18612
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 3.2 3.42 100 0.536 0.572 0.198 0.898 8.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT AF-O58994-F1 3.2 75.83 17639 928 100 0.17247 0.16916 0.23723 0.2106 RANDOM 48.149
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] -2.4 2.95 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.242 r_dihedral_angle_2_deg 9.88 r_dihedral_angle_1_deg 7.509 r_long_range_B_refined 7.293 r_long_range_B_other 7.293 r_scangle_other 4.882 r_mcangle_it 4.042 r_mcangle_other 4.042 r_scbond_it 2.882 r_scbond_other 2.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.242 r_dihedral_angle_2_deg 9.88 r_dihedral_angle_1_deg 7.509 r_long_range_B_refined 7.293 r_long_range_B_other 7.293 r_scangle_other 4.882 r_mcangle_it 4.042 r_mcangle_other 4.042 r_scbond_it 2.882 r_scbond_other 2.881 r_mcbond_it 2.434 r_mcbond_other 2.434 r_angle_refined_deg 1.407 r_angle_other_deg 0.434 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6610 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 59
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction