☰ Navigation Tabs
Crystal structure of vanillin dehydrogenase with covalently bound vanillin and cofactor NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18 % w/v PEG 5000 MME, 0.2 M Ammonium sulfate, 0.1 M MES 6.5, 3 mM vanillin, 10 mM NAD+
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.069 α = 90 b = 150.837 β = 93.877 c = 150.404 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 DECTRIS EIGER2 XE 16M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 2.41 150.06 91 0.322 0.129 0.982 5.5 7.2 107071
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 2.41 2.588 67.3 1.373 0.543 0.553 1.6 7.4
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 2.41 150.06 107069 5571 67.847 0.197 0.1956 0.1955 0.2264 0.2264 RANDOM 32.469
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] -0.798 -0.667 0.509 0.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.784 r_dihedral_angle_3_deg 14.681 r_dihedral_angle_2_deg 8.319 r_dihedral_angle_1_deg 6.398 r_lrange_it 5.925 r_scangle_it 4.478 r_scbond_it 2.905 r_mcangle_it 2.806 r_angle_refined_deg 1.935 r_mcbond_it 1.716
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.784 r_dihedral_angle_3_deg 14.681 r_dihedral_angle_2_deg 8.319 r_dihedral_angle_1_deg 6.398 r_lrange_it 5.925 r_scangle_it 4.478 r_scbond_it 2.905 r_mcangle_it 2.806 r_angle_refined_deg 1.935 r_mcbond_it 1.716 r_symmetry_xyhbond_nbd_refined 0.31 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.286 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.117 r_ncsr_local_group_19 0.046 r_ncsr_local_group_3 0.045 r_ncsr_local_group_14 0.045 r_ncsr_local_group_21 0.044 r_ncsr_local_group_2 0.043 r_ncsr_local_group_20 0.043 r_ncsr_local_group_1 0.041 r_ncsr_local_group_9 0.041 r_ncsr_local_group_16 0.041 r_ncsr_local_group_8 0.039 r_ncsr_local_group_22 0.039 r_ncsr_local_group_7 0.038 r_ncsr_local_group_17 0.038 r_ncsr_local_group_15 0.037 r_ncsr_local_group_18 0.037 r_ncsr_local_group_4 0.036 r_ncsr_local_group_6 0.036 r_ncsr_local_group_5 0.035 r_ncsr_local_group_12 0.034 r_ncsr_local_group_10 0.033 r_ncsr_local_group_11 0.032 r_ncsr_local_group_26 0.032 r_ncsr_local_group_23 0.031 r_ncsr_local_group_28 0.028 r_ncsr_local_group_25 0.027 r_ncsr_local_group_13 0.025 r_ncsr_local_group_27 0.024 r_ncsr_local_group_24 0.016 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27366 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 480
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing