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Crystal structure of aminoaldehyde dehydrogenase 2 from Pisum sativum (PsAMADH2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 18% PEG 4000, 10% isopropanol, 0.5% beta-octylglucoside, 5mM NAD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.25 α = 90 b = 86.73 β = 90 c = 179.16 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 CCD ADSC QUANTUM 4 2009-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.15 30 99.2 0.059 14.7 57015 56568 2 1 42.059
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 2.15 2.26 99.5 0.442 3.4
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 3IWK 2.15 25 53715 2827 100 0.23646 0.23364 0.2383 0.28935 0.2947 RANDOM 39.288
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] -1.45 4.82 -3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.179 r_dihedral_angle_4_deg 19.634 r_dihedral_angle_3_deg 16.501 r_dihedral_angle_1_deg 5.298 r_scangle_it 1.995 r_angle_refined_deg 1.168 r_scbond_it 1.143 r_mcangle_it 0.722 r_mcbond_it 0.372 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.179 r_dihedral_angle_4_deg 19.634 r_dihedral_angle_3_deg 16.501 r_dihedral_angle_1_deg 5.298 r_scangle_it 1.995 r_angle_refined_deg 1.168 r_scbond_it 1.143 r_mcangle_it 0.722 r_mcbond_it 0.372 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7622 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 98
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling