☰ Navigation Tabs
Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Covalent complex with 2-deoxyribose.
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 35% tascimate
Crystal Properties Matthews coefficient Solvent content 3.77 67.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.461 α = 90 b = 148.461 β = 90 c = 148.461 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 2.37 60.61 100 0.06 0.01 1 42.5 41.2 22224
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 2.37 2.46 0.96 0.22 0.95 5.1
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 2.371 60.61 22212 1115 99.982 0.201 0.199 0.2043 0.2284 0.2327 63.329
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 16.146 r_dihedral_angle_6_deg 13.764 r_dihedral_angle_2_deg 9.856 r_lrange_other 9.613 r_lrange_it 9.61 r_scangle_it 8.36 r_scangle_other 8.358 r_mcangle_it 7.331 r_mcangle_other 7.329 r_dihedral_angle_1_deg 6.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.146 r_dihedral_angle_6_deg 13.764 r_dihedral_angle_2_deg 9.856 r_lrange_other 9.613 r_lrange_it 9.61 r_scangle_it 8.36 r_scangle_other 8.358 r_mcangle_it 7.331 r_mcangle_other 7.329 r_dihedral_angle_1_deg 6.67 r_scbond_it 6.247 r_scbond_other 6.245 r_mcbond_it 5.788 r_mcbond_other 5.783 r_angle_refined_deg 1.661 r_angle_other_deg 0.578 r_nbd_other 0.252 r_nbd_refined 0.22 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.129 r_symmetry_nbd_refined 0.114 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.091 r_ncsr_local_group_1 0.075 r_bond_refined_d 0.007 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 2523 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing