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1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Pseudomonas putida in Complex with FAD and Adenosine-5'-monophosphate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TR3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 Protein: 16.3 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1mM FAD;Screen: JCSG+ (G11), 2M Ammonium sulfate, 0.01M Bis-Tris HCl (pH 5.5);Cryo: 2M Ammonim sulfate, 25% sucrose.
Crystal Properties Matthews coefficient Solvent content 3.02 59.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.936 α = 90 b = 113.089 β = 90 c = 120.695 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) 2017-07-12 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) 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 1.83 30 99.9 0.05 0.05 0.022 34.2 6.2 107766 -3 31.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 100 0.814 0.814 0.353 0.813 2.3 6.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5TR3 1.83 29.83 102097 5468 99.85 0.17735 0.17612 0.20069 0.2171 RANDOM 41.157
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] 0.32 -2.39 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.775 r_dihedral_angle_3_deg 9.637 r_dihedral_angle_4_deg 7.083 r_long_range_B_refined 5.808 r_long_range_B_other 5.698 r_scangle_other 3.326 r_dihedral_angle_1_deg 2.911 r_mcangle_it 2.129 r_mcangle_other 2.129 r_scbond_it 2.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.775 r_dihedral_angle_3_deg 9.637 r_dihedral_angle_4_deg 7.083 r_long_range_B_refined 5.808 r_long_range_B_other 5.698 r_scangle_other 3.326 r_dihedral_angle_1_deg 2.911 r_mcangle_it 2.129 r_mcangle_other 2.129 r_scbond_it 2.123 r_scbond_other 2.116 r_angle_refined_deg 1.429 r_mcbond_it 1.38 r_mcbond_other 1.38 r_angle_other_deg 0.848 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 6946 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing