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Crystal structure of aminoaldehyde dehydrogenase 1 from Pisum sativum (PsAMADH1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES pH 7.5, 13% PEG 6000, 5% 2-methyl-2,4-pentanediol, 5mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.41 α = 90 b = 216.87 β = 98.02 c = 205.76 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 ADSC QUANTUM 315r 2008-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.98 ESRF ID29
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 2.4 50 99.7 0.103 14.06 291593 290858 2 1 40.72
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 2.4 2.53 99.5 0.622 3.7
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 1CW3 2.4 47.84 276314 14543 100 0.20198 0.19979 0.2 0.2436 0.2438 RANDOM 34.693
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] 1.72 0.12 0.82 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.334 r_dihedral_angle_4_deg 18.989 r_dihedral_angle_3_deg 17.913 r_dihedral_angle_1_deg 5.245 r_scangle_it 1.742 r_angle_refined_deg 1.114 r_scbond_it 0.972 r_mcangle_it 0.698 r_mcbond_it 0.358 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.334 r_dihedral_angle_4_deg 18.989 r_dihedral_angle_3_deg 17.913 r_dihedral_angle_1_deg 5.245 r_scangle_it 1.742 r_angle_refined_deg 1.114 r_scbond_it 0.972 r_mcangle_it 0.698 r_mcbond_it 0.358 r_chiral_restr 0.08 r_bond_refined_d 0.007 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 45663 Nucleic Acid Atoms Solvent Atoms 1997 Heterogen Atoms 645
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction