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Structure of the apo form of a Zingiber officinale double bond reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HFN model generated by Robetta server with structure 4HFN as target
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 60 mM KCN, 28% PEG 2000 MME, 3 mM NaN3, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.93 α = 80.15 b = 76.34 β = 89.97 c = 93.45 γ = 85.66
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 2013-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.58 46.03 97.7 0.072 12.88 3.3 42573 42573 -3 49.681
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.65 86.3 0.539 2.19
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 model generated by Robetta server with structure 4HFN as target 2.58 46.03 42573 42573 2131 97.63 0.2309 0.2309 0.2281 0.2295 0.2817 0.2833 RANDOM 47.4358
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] 0.44 0.15 0.4 -0.36 0.75 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.075 r_dihedral_angle_4_deg 21.788 r_dihedral_angle_3_deg 16.032 r_dihedral_angle_1_deg 6.411 r_angle_other_deg 3.771 r_mcangle_it 1.804 r_angle_refined_deg 1.674 r_mcbond_it 1.065 r_mcbond_other 1.065 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.075 r_dihedral_angle_4_deg 21.788 r_dihedral_angle_3_deg 16.032 r_dihedral_angle_1_deg 6.411 r_angle_other_deg 3.771 r_mcangle_it 1.804 r_angle_refined_deg 1.674 r_mcbond_it 1.065 r_mcbond_other 1.065 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9119 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction