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Crystal structure of ALDH1A2 in complex with KyA33
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ALJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M L-Proline, 0.1 M HEPES-NaOH pH 7.50, 10% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.639 α = 90 b = 140.045 β = 93.93 c = 84.775 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 PILATUS3 2M 2022-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
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 1.4 30 98.5 0.105 0.113 0.043 0.996 9.3 6.8 365896
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 1.4 1.48 97 0.635 0.686 0.258 0.801 7.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.4 29.82 346817 18629 98.14 0.15682 0.15573 0.1561 0.1767 0.1772 RANDOM 12.619
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] 0.82 -0.07 0.06 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.517 r_dihedral_angle_1_deg 6.449 r_long_range_B_refined 5.729 r_long_range_B_other 4.981 r_dihedral_angle_2_deg 4.213 r_scangle_other 1.828 r_scbond_it 1.195 r_scbond_other 1.195 r_angle_refined_deg 1.019 r_mcangle_it 0.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.517 r_dihedral_angle_1_deg 6.449 r_long_range_B_refined 5.729 r_long_range_B_other 4.981 r_dihedral_angle_2_deg 4.213 r_scangle_other 1.828 r_scbond_it 1.195 r_scbond_other 1.195 r_angle_refined_deg 1.019 r_mcangle_it 0.966 r_mcangle_other 0.966 r_mcbond_it 0.604 r_mcbond_other 0.604 r_angle_other_deg 0.367 r_chiral_restr 0.054 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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 15250 Nucleic Acid Atoms Solvent Atoms 3194 Heterogen Atoms 224
Software Software Software Name Purpose DIALS data reduction SCALA data scaling REFMAC phasing REFMAC refinement