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Crystal structure of Malus domestica Double Bond Reductase (MdDBR) ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (w/v) MPD, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.03 M sodium chloride, 0.03 M sodium bromide, 0.03 M sodium iodide in 0.1 M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.491 α = 90 b = 68.611 β = 90 c = 145.969 γ = 90
Symmetry Space Group I 2 2 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 PILATUS3 S 6M 2019-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.36 48.52 99.5 0.99 12.1 9.6 72885
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.39 0.493
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 6YSB 1.36 48.52 69315 3570 99.46 0.1446 0.1429 0.1429 0.1793 0.1797 RANDOM 19.999
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] 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.972 r_dihedral_angle_4_deg 17.043 r_dihedral_angle_3_deg 13.851 r_dihedral_angle_1_deg 7.136 r_rigid_bond_restr 4.051 r_angle_refined_deg 2.011 r_angle_other_deg 1.566 r_chiral_restr 0.126 r_bond_refined_d 0.017 r_gen_planes_refined 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.972 r_dihedral_angle_4_deg 17.043 r_dihedral_angle_3_deg 13.851 r_dihedral_angle_1_deg 7.136 r_rigid_bond_restr 4.051 r_angle_refined_deg 2.011 r_angle_other_deg 1.566 r_chiral_restr 0.126 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2640 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing