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Structure of TbALDH3 complexed with NAD and AN3057 aldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 100 mM Bis-Tris pH 5.5, 0.2 M LiSO4, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.168 α = 90 b = 62.524 β = 100.08 c = 92.974 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 CCD RIGAKU SATURN 944+ 2016-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 46.56 97.6 0.074 0.989 12.9 3.1 34306 7.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 93.9 0.112 0.968 8 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5MYP 2.5 46.56 32560 1736 85.88 0.23613 0.23389 0.2716 0.27807 0.3316 RANDOM 26.145
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] -7.85 -4.06 -13.22 21.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.399 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_4_deg 14.981 r_dihedral_angle_1_deg 6.651 r_long_range_B_refined 1.967 r_long_range_B_other 1.954 r_angle_refined_deg 1.551 r_angle_other_deg 0.991 r_scangle_other 0.346 r_scbond_it 0.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.399 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_4_deg 14.981 r_dihedral_angle_1_deg 6.651 r_long_range_B_refined 1.967 r_long_range_B_other 1.954 r_angle_refined_deg 1.551 r_angle_other_deg 0.991 r_scangle_other 0.346 r_scbond_it 0.241 r_scbond_other 0.241 r_chiral_restr 0.082 r_mcbond_other 0.041 r_mcbond_it 0.04 r_mcangle_other 0.016 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_it 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 7512 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing