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2.9 Angstrom Resolution Crystal Structure of Gamma-Aminobutyraldehyde Dehydrogenase from Salmonella typhimurium.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Protein: 7.4 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3;
Screen: Classics II (D7), 0.1M Bis-Tris (pH=6.5), 25% (w/v) PEG 3350;
Crystal Properties Matthews coefficient Solvent content 2.36 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.891 α = 82.76 b = 87.8 β = 77.91 c = 145.07 γ = 72.86
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 MARMOSAIC 225 mm CCD C(111) 2010-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 30 98.7 0.066 0.066 0.094 0.066 11.7 2 82131 -3 62.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 98.2 0.416 0.416 0.589 0.416 0.719 1.9 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 1WND 2.9 29.73 77939 4155 98.36 0.19016 0.18859 0.1896 0.21914 0.2207 RANDOM 63.68
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] 0.39 -2.19 4.06 -0.03 -3.1 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.623 r_dihedral_angle_4_deg 15.537 r_dihedral_angle_3_deg 9.621 r_long_range_B_refined 7.762 r_mcangle_it 3.497 r_scbond_it 2.78 r_mcbond_it 2.077 r_dihedral_angle_1_deg 1.564 r_angle_refined_deg 1.486 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.623 r_dihedral_angle_4_deg 15.537 r_dihedral_angle_3_deg 9.621 r_long_range_B_refined 7.762 r_mcangle_it 3.497 r_scbond_it 2.78 r_mcbond_it 2.077 r_dihedral_angle_1_deg 1.564 r_angle_refined_deg 1.486 r_chiral_restr 0.099 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28728 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing