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Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AYX pdb entry 1AYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 295 50 mM acetate buffer, 15% PEG 8K, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.58 α = 90 b = 85.35 β = 90 c = 97.51 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 AREA DETECTOR MARRESEARCH mirrors 2002-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9096 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 1.6 10 94.5 0.043 17.5 3.49 59266 1 1 15.6
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 1.6 1.62 0.144 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1AYX 1.6 10 2 56255 3010 94.04 0.12 0.11975 0.11762 0.12 0.15958 0.1597 RANDOM 12.659
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] -0.21 0.48 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.733 r_scangle_it 3.318 r_sphericity_free 2.593 r_scbond_it 2.237 r_sphericity_bonded 1.82 r_angle_refined_deg 1.609 r_mcangle_it 1.535 r_rigid_bond_restr 1.184 r_angle_other_deg 1.047 r_mcbond_it 0.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.733 r_scangle_it 3.318 r_sphericity_free 2.593 r_scbond_it 2.237 r_sphericity_bonded 1.82 r_angle_refined_deg 1.609 r_mcangle_it 1.535 r_rigid_bond_restr 1.184 r_angle_other_deg 1.047 r_mcbond_it 0.938 r_symmetry_vdw_other 0.274 r_nbd_other 0.248 r_symmetry_hbond_refined 0.218 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.21 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.159 r_nbtor_other 0.085 r_gen_planes_refined 0.015 r_gen_planes_other 0.015 r_bond_refined_d 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3870 Nucleic Acid Atoms Solvent Atoms 810 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing