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Crystal structure of Oryza sativa Os4BGlu18 monolignol beta-glucosidase with delta-gluconolactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RGL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 288 19% PEG 3350, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288 K
Crystal Properties Matthews coefficient Solvent content 2.05 39.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.109 α = 90 b = 83.831 β = 90 c = 207.448 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 RAYONIX MX300HE 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.000 NSRRC BL15A1
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 2.1 30 98.9 0.998 26.3 6.6 53787
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 2.1 2.18 0.987
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 2RGL 2.1 30 50803 2676 98.86 0.1467 0.1451 0.1578 0.1771 0.1868 RANDOM 19.825
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] 0.07 1.02 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 18.426 r_dihedral_angle_3_deg 11.746 r_dihedral_angle_1_deg 6.142 r_angle_refined_deg 1.35 r_angle_other_deg 0.959 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 18.426 r_dihedral_angle_3_deg 11.746 r_dihedral_angle_1_deg 6.142 r_angle_refined_deg 1.35 r_angle_other_deg 0.959 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7715 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing