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Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii (apo).
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 20 mM NaH2PO4 buffer; 0.2M sodium citrate; 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.83 67.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.27 α = 90 b = 149.27 β = 90 c = 149.27 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 2024-01-20 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 2.79 60.94 100 0.15 0.03 1 22.6 40.8 13954 75
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 2.79 2.94 2.2 0.49 0.82 2.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.79 52.831 13951 723 99.971 0.175 0.1717 0.1744 0.2374 0.2321 RANDOM 77.264
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 17.396 r_dihedral_angle_6_deg 13.954 r_lrange_it 11.357 r_lrange_other 11.355 r_scangle_it 10.688 r_scangle_other 10.686 r_dihedral_angle_2_deg 10.252 r_mcangle_it 8.882 r_mcangle_other 8.882 r_scbond_it 8.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.396 r_dihedral_angle_6_deg 13.954 r_lrange_it 11.357 r_lrange_other 11.355 r_scangle_it 10.688 r_scangle_other 10.686 r_dihedral_angle_2_deg 10.252 r_mcangle_it 8.882 r_mcangle_other 8.882 r_scbond_it 8.388 r_scbond_other 8.388 r_mcbond_it 6.963 r_mcbond_other 6.963 r_dihedral_angle_1_deg 6.382 r_angle_refined_deg 1.838 r_angle_other_deg 0.635 r_nbd_other 0.251 r_nbd_refined 0.216 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.192 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.098 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_1 0.08 r_symmetry_xyhbond_nbd_refined 0.043 r_chiral_restr_other 0.038 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2500 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing