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Structure of inactive mutant of Strictosidine Glucosidase in complex with strictosidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JF7 PDB ENTRY 2JF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.35 M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH 4.6 11% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.69 4.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159 α = 90 b = 159 β = 90 c = 102.9 γ = 90
Symmetry Space Group P 4 21 2
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.82 20 98.4 0.06 20.2 28.2 32951 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.97 99.1 0.11 7.6 28
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 PDB ENTRY 2JF7 2.82 20 30623 1621 99.1 0.225 0.222 0.2174 0.28 0.2776 RANDOM 9
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] 0.43 0.43 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.77 r_dihedral_angle_4_deg 22.907 r_dihedral_angle_3_deg 22.61 r_dihedral_angle_1_deg 6.83 r_scangle_it 3.331 r_scbond_it 2.186 r_angle_refined_deg 1.624 r_mcangle_it 0.863 r_mcbond_it 0.462 r_nbd_refined 0.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.77 r_dihedral_angle_4_deg 22.907 r_dihedral_angle_3_deg 22.61 r_dihedral_angle_1_deg 6.83 r_scangle_it 3.331 r_scbond_it 2.186 r_angle_refined_deg 1.624 r_mcangle_it 0.863 r_mcbond_it 0.462 r_nbd_refined 0.334 r_gen_planes_other 0.257 r_symmetry_vdw_refined 0.238 r_xyhbond_nbd_refined 0.202 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.114 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7607 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing