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Crystal structure of Spodoptera frugiperda Beta-glycosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 291 100 mM Bis-Tris-HCl, 100 mM NaCL, 22% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 50.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.825 α = 93.16 b = 64.994 β = 92.04 c = 257.189 γ = 112.18
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2014-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 60 91.4 0.08 0.095 0.05 12.1 3.3 173155
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 90 0.539 0.65 0.356 0.709 3.2 17076
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 3VIF 2.09 49.75 164477 8675 90.99 0.1952 0.1924 0.1983 0.2498 0.2532 RANDOM 42.899
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.203 r_dihedral_angle_4_deg 18.654 r_dihedral_angle_3_deg 14.86 r_dihedral_angle_1_deg 5.997 r_mcangle_it 3.275 r_mcbond_it 2.073 r_mcbond_other 2.072 r_angle_refined_deg 1.208 r_angle_other_deg 0.826 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.203 r_dihedral_angle_4_deg 18.654 r_dihedral_angle_3_deg 14.86 r_dihedral_angle_1_deg 5.997 r_mcangle_it 3.275 r_mcbond_it 2.073 r_mcbond_other 2.072 r_angle_refined_deg 1.208 r_angle_other_deg 0.826 r_chiral_restr 0.097 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23565 Nucleic Acid Atoms Solvent Atoms 1318 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building