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Crystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin and trans-zeatin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 292 1.4 M sodium citrate pH 6.3
Crystal Properties Matthews coefficient Solvent content 3.24 62.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.4 α = 90 b = 74.4 β = 90 c = 67.31 γ = 120
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 2012-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.0000000 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.57 46.59 99.7 0.037 0.041 0.999 22.2 4.984 29524 -3 31.574
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.66 98.4 0.744 0.834 0.789 2.01 4.892
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 2qim 1.57 46.59 28468 1057 99.68 0.1858 0.185 0.2059 0.2091 RANDOM 32.201
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] -0.91 -0.91 -0.91 2.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.583 r_dihedral_angle_3_deg 15.508 r_dihedral_angle_1_deg 7.039 r_angle_refined_deg 1.866 r_angle_other_deg 0.791 r_dihedral_angle_4_deg 0.424 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.583 r_dihedral_angle_3_deg 15.508 r_dihedral_angle_1_deg 7.039 r_angle_refined_deg 1.866 r_angle_other_deg 0.791 r_dihedral_angle_4_deg 0.424 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1162 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing