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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 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.141 α = 90 b = 130.454 β = 94.46 c = 94.836 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 2016-05-19 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 1.98 30 93.9 0.101 0.117 0.057 11.8 3.9 109351
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 1.981 2.032 93.2 0.617 0.717 0.361 0.714 3.7
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 1.98 30 103832 5439 92.7 0.16962 0.16745 0.1776 0.21143 0.218 RANDOM 27.622
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] 1.1 0.37 -0.5 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 17.072 r_dihedral_angle_3_deg 14.736 r_dihedral_angle_1_deg 7.055 r_long_range_B_refined 5.301 r_long_range_B_other 5.282 r_scangle_other 4.205 r_scbond_it 2.927 r_scbond_other 2.927 r_mcangle_it 2.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 17.072 r_dihedral_angle_3_deg 14.736 r_dihedral_angle_1_deg 7.055 r_long_range_B_refined 5.301 r_long_range_B_other 5.282 r_scangle_other 4.205 r_scbond_it 2.927 r_scbond_other 2.927 r_mcangle_it 2.566 r_mcangle_other 2.566 r_mcbond_it 1.977 r_mcbond_other 1.974 r_angle_refined_deg 1.652 r_angle_other_deg 1.035 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11659 Nucleic Acid Atoms Solvent Atoms 814 Heterogen Atoms 386
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction PHENIX phasing