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Crystal of Raucaffricine Glucosidase in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ATD PDB ENTRY 4ATD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10% PEG4000, 0.3 M AMSO4
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.146 α = 90 b = 127.954 β = 90 c = 215.204 γ = 90
Symmetry Space Group I 2 2 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 MONOCHROMATOR 2006-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.4 20 100 0.15 23.8 15 56755 -3 38.838
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 2.4 2.44 100 0.76 4.86 14.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4ATD 2.4 19.86 54787 1017 99.97 0.16502 0.16437 0.1989 0.1794 RANDOM 43.136
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] 0.06 -0.09 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.022 r_dihedral_angle_4_deg 21.016 r_dihedral_angle_3_deg 14.634 r_dihedral_angle_1_deg 6.205 r_scangle_it 5.508 r_scbond_it 4.016 r_angle_refined_deg 1.684 r_mcangle_it 1.562 r_mcbond_it 0.829 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.022 r_dihedral_angle_4_deg 21.016 r_dihedral_angle_3_deg 14.634 r_dihedral_angle_1_deg 6.205 r_scangle_it 5.508 r_scbond_it 4.016 r_angle_refined_deg 1.684 r_mcangle_it 1.562 r_mcbond_it 0.829 r_chiral_restr 0.11 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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 7532 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling Auto-Rickshaw phasing