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Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Bis-Tris pH6.5, 26% PEG MME550, 0.15M CaCl2
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.787 α = 90 b = 129.911 β = 94.44 c = 95.162 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 CCD RAYONIX MX300HE 2016-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.4 50 90.6 0.079 0.094 0.049 16.8 3 59786
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 2.4 2.44 81.4 0.184 0.23 0.135 0.86 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 30 56703 3061 90.59 0.1557 0.1528 0.1619 0.2077 0.2152 RANDOM 25.898
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] 1.74 -0.35 -0.03 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.653 r_dihedral_angle_4_deg 18.399 r_dihedral_angle_3_deg 13.718 r_dihedral_angle_1_deg 6.65 r_angle_refined_deg 1.679 r_angle_other_deg 0.977 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.653 r_dihedral_angle_4_deg 18.399 r_dihedral_angle_3_deg 13.718 r_dihedral_angle_1_deg 6.65 r_angle_refined_deg 1.679 r_angle_other_deg 0.977 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11660 Nucleic Acid Atoms Solvent Atoms 552 Heterogen Atoms 434
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction PHENIX phasing