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Crystal structure of the ribonucleoside hydrolase C from Lactobacillus reuteri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.112 α = 90 b = 81.53 β = 95.76 c = 86.847 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 100 PIXEL RIGAKU HyPix-6000HE 2022-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 1.9 63.38 99.8 0.082 0.091 0.039 0.914 19.5 6.4 91739
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 1.9 1.93 100 0.347 0.377 0.146 0.956 6.6
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 (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 1.9 63.38 87159 4557 99.62 0.16996 0.1684 0.1785 0.20077 0.2102 RANDOM 22.401
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] -1.39 0.62 -0.26 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.989 r_dihedral_angle_4_deg 20.232 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_1_deg 7.475 r_long_range_B_refined 5.705 r_long_range_B_other 5.638 r_scangle_other 4.583 r_mcangle_other 3.585 r_mcangle_it 3.583 r_scbond_it 3.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.989 r_dihedral_angle_4_deg 20.232 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_1_deg 7.475 r_long_range_B_refined 5.705 r_long_range_B_other 5.638 r_scangle_other 4.583 r_mcangle_other 3.585 r_mcangle_it 3.583 r_scbond_it 3.201 r_scbond_other 3.199 r_mcbond_it 2.591 r_mcbond_other 2.581 r_angle_refined_deg 1.835 r_angle_other_deg 1.473 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.006 r_bond_other_d 0.005 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 8847 Nucleic Acid Atoms Solvent Atoms 766 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction