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Structure of the binary complex of a zingiber officinale double bond reductase in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 21% PEG 1450, 100mM PCB, 3mM NaN3, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.31 46.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.66 α = 90 b = 78.406 β = 90 c = 155.706 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 225 mm CCD PT COATED SI MIRRORS 2013-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 78.037 99.3 0.091 12.8 4.5 43868 43868 -3
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) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 99.9 0.745 0.745 0.843 0.389 0.9 4.6 6310
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4MKR 2.1 55.31 43787 43787 2250 99.07 0.1964 0.1964 0.193 0.2007 0.2598 0.2632 RANDOM 39.061
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 0.45 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.737 r_dihedral_angle_3_deg 14.688 r_dihedral_angle_4_deg 12.697 r_dihedral_angle_1_deg 7.032 r_mcangle_it 3.152 r_mcbond_it 2.13 r_mcbond_other 2.13 r_angle_refined_deg 1.815 r_angle_other_deg 0.848 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.737 r_dihedral_angle_3_deg 14.688 r_dihedral_angle_4_deg 12.697 r_dihedral_angle_1_deg 7.032 r_mcangle_it 3.152 r_mcbond_it 2.13 r_mcbond_other 2.13 r_angle_refined_deg 1.815 r_angle_other_deg 0.848 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5391 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 96
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction