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Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 293.15 reservoir solution: 1.6 M NaH2PO4/K2HPO4 buffer, pH 8.1 (K2HPO4 was titrated with NaH2PO4 to pH 8.1)
Crystal Properties Matthews coefficient Solvent content 2.91 57.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.035 α = 90 b = 168.939 β = 90 c = 61.279 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.84 48.38 98.1 10.78 4.54 105160 36.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.95 97.4 0.87
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 1ZMD 1.84 48.38 103058 2101 98.1 0.1823 0.1814 0.1893 0.2261 0.2297 RANDOM 39.357
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] -0.71 -0.42 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.234 r_dihedral_angle_3_deg 15.353 r_dihedral_angle_4_deg 14.945 r_dihedral_angle_1_deg 6.661 r_mcangle_it 2.643 r_angle_refined_deg 2.427 r_mcbond_it 1.728 r_mcbond_other 1.722 r_angle_other_deg 1.184 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.234 r_dihedral_angle_3_deg 15.353 r_dihedral_angle_4_deg 14.945 r_dihedral_angle_1_deg 6.661 r_mcangle_it 2.643 r_angle_refined_deg 2.427 r_mcbond_it 1.728 r_mcbond_other 1.722 r_angle_other_deg 1.184 r_chiral_restr 0.154 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7123 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XDS data scaling MOLREP phasing