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Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Y7F/D72N mutant with cytidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 25% tascimate, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.9 68.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.134 α = 90 b = 150.134 β = 90 c = 150.134 γ = 90
Symmetry Space Group I 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS EIGER2 XE 16M 2024-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976277 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.48 61.37 100 0.16 0.14 1 26.1 41.6 20103 47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.58 1.56 0.34 0.9 3.9
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 2.48 61.37 19055 1044 99.97 0.16446 0.16316 0.1702 0.18773 0.1932 RANDOM 50.313
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.983 r_dihedral_angle_2_deg 10.853 r_long_range_B_refined 9.499 r_long_range_B_other 9.474 r_scangle_other 8.092 r_dihedral_angle_1_deg 6.343 r_scbond_it 6.078 r_scbond_other 6.076 r_mcangle_it 5.839 r_mcangle_other 5.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.983 r_dihedral_angle_2_deg 10.853 r_long_range_B_refined 9.499 r_long_range_B_other 9.474 r_scangle_other 8.092 r_dihedral_angle_1_deg 6.343 r_scbond_it 6.078 r_scbond_other 6.076 r_mcangle_it 5.839 r_mcangle_other 5.839 r_mcbond_it 4.548 r_mcbond_other 4.548 r_angle_refined_deg 1.7 r_angle_other_deg 0.622 r_chiral_restr 0.102 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 2519 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing