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crystal structure of NAD-dependent glycoside hydrolase from Arthrobacter sp. U41 in complex with NAD+ cofactor and citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 protein was incubated with 2m M NAD+. crystals were grown in wells containing 1.8 M triammonium citrate pH7
Crystal Properties Matthews coefficient Solvent content 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.863 α = 90 b = 72.817 β = 90 c = 197.307 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 PIXEL DECTRIS EIGER2 XE 16M 2023-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
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 1.95 49.33 100 0.173 0.18 0.048 0.998 11.9 13.7 60807
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 1.95 2 100 1.251 1.298 0.343 0.911 14.2
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 1.95 49.3 57694 3029 99.98 0.2001 0.19805 0.2078 0.23857 0.2443 RANDOM 29.385
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] 6.34 -3.99 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.367 r_dihedral_angle_2_deg 15.251 r_dihedral_angle_1_deg 7.813 r_long_range_B_refined 6.064 r_long_range_B_other 6.064 r_scangle_other 4.55 r_mcangle_it 3.258 r_mcangle_other 3.258 r_scbond_it 3.227 r_scbond_other 3.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.367 r_dihedral_angle_2_deg 15.251 r_dihedral_angle_1_deg 7.813 r_long_range_B_refined 6.064 r_long_range_B_other 6.064 r_scangle_other 4.55 r_mcangle_it 3.258 r_mcangle_other 3.258 r_scbond_it 3.227 r_scbond_other 3.224 r_mcbond_it 2.34 r_mcbond_other 2.339 r_angle_refined_deg 1.336 r_angle_other_deg 0.455 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 5533 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing