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Crystal structure of strictosidine glucosidase in complex with inhibitor-1
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 10% PEG4000, 0.3 M AMSO4, 0.1M NAOAC, PH 5.0
Crystal Properties Matthews coefficient Solvent content 3.04 59.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.219 α = 90 b = 159.219 β = 90 c = 110.974 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 ADSC CCD MIRROR 2012-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U SSRF BL17U
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 2.5 2.63 96.6 0.12 16.34 9.1 48795 -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 2.5 2.63 93.1 0.33 6.48 7.3
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 2.5 19.73 47887 1009 98.68 0.2584 0.25804 0.2648 0.27567 0.2565 RANDOM 39.628
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] -0.12 -0.12 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.757 r_dihedral_angle_4_deg 24.366 r_dihedral_angle_3_deg 19.011 r_dihedral_angle_1_deg 7.618 r_scangle_it 3.251 r_scbond_it 2.248 r_angle_refined_deg 2.061 r_mcangle_it 1.135 r_mcbond_it 0.654 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.757 r_dihedral_angle_4_deg 24.366 r_dihedral_angle_3_deg 19.011 r_dihedral_angle_1_deg 7.618 r_scangle_it 3.251 r_scbond_it 2.248 r_angle_refined_deg 2.061 r_mcangle_it 1.135 r_mcbond_it 0.654 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 7592 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Auto-Rickshaw phasing