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2.5 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Pseudomonas putida in Complex with FAD.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 13.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1mM FAD; Screen: Classics II(F10), 0.2M Sodim chloride, 0.01M Tris HCl (pH 6.5), 25% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.75 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.886 α = 90 b = 132.113 β = 90 c = 158.132 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 MARMOSAIC 300 mm CCD C(111) 2016-10-05 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) 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 2.5 30 99.9 0.075 0.075 20.1 4.9 42116 -3 51.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 100 0.632 0.837 2.6 4.9
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 3LAD 2.5 29.42 40007 2044 99.77 0.22729 0.2254 0.2291 0.26422 0.2655 RANDOM 60.399
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] -1.47 7.17 -5.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.201 r_dihedral_angle_4_deg 14.204 r_dihedral_angle_3_deg 10.771 r_long_range_B_refined 5.665 r_long_range_B_other 5.651 r_scangle_other 2.822 r_mcangle_it 2.763 r_mcangle_other 2.763 r_dihedral_angle_1_deg 1.998 r_scbond_it 1.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.201 r_dihedral_angle_4_deg 14.204 r_dihedral_angle_3_deg 10.771 r_long_range_B_refined 5.665 r_long_range_B_other 5.651 r_scangle_other 2.822 r_mcangle_it 2.763 r_mcangle_other 2.763 r_dihedral_angle_1_deg 1.998 r_scbond_it 1.758 r_scbond_other 1.754 r_mcbond_it 1.733 r_mcbond_other 1.732 r_angle_refined_deg 1.459 r_angle_other_deg 0.877 r_chiral_restr 0.081 r_gen_planes_refined 0.023 r_gen_planes_other 0.02 r_bond_refined_d 0.009 r_bond_other_d 0.001 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 6924 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing