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Human aldehyde dehydrogenase 1A3 complexed with NAD(+) and retinoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 20% PEG 3350, 0.24 M Na2 malonate pH 7.0, 10 mM TCEP hydrochloride
Crystal Properties Matthews coefficient Solvent content 2.76 55.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.656 α = 90 b = 159.785 β = 93.69 c = 177.647 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 PSI PILATUS 6M 2014-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.899 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 49.57 98.29 0.1822 5.35 3.6 364821 100139
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 97.44 0.55 1.46 3.2
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 1BXS 2.9 49.57 95090 5047 98.27 0.23118 0.22808 0.2278 0.28923 0.2864 RANDOM 43.479
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] 0.05 0.02 0.01 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.533 r_dihedral_angle_4_deg 18.811 r_dihedral_angle_3_deg 16.26 r_dihedral_angle_1_deg 6.334 r_long_range_B_refined 5.208 r_long_range_B_other 5.208 r_scangle_other 4.122 r_mcangle_it 3.47 r_mcangle_other 3.47 r_scbond_it 2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.533 r_dihedral_angle_4_deg 18.811 r_dihedral_angle_3_deg 16.26 r_dihedral_angle_1_deg 6.334 r_long_range_B_refined 5.208 r_long_range_B_other 5.208 r_scangle_other 4.122 r_mcangle_it 3.47 r_mcangle_other 3.47 r_scbond_it 2.85 r_scbond_other 2.85 r_mcbond_it 2.279 r_mcbond_other 2.278 r_angle_other_deg 1.936 r_angle_refined_deg 1.425 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 29489 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 440
Software Software Software Name Purpose REFMAC refinement PHASER phasing SCALA data scaling XDS data reduction