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Glucoamylase from Saccharomycopsis fibuligera at atomic resolution
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 acatate buffer, 15% PEG 8K, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.901 α = 90 b = 85.696 β = 90 c = 98.237 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 BW7B 0.834 EMBL/DESY, HAMBURG BW7B
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 1.1 15 93.5 0.059 16.9 184868 208793 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.1 1.129 93.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1.1 14.8 2 184868 168888 8959 91.43 0.146 0.14586 0.14504 0.1456 0.16119 0.1616 RANDOM 12.257
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] 0.24 -0.16 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.641 r_scangle_it 2.689 r_sphericity_bonded 2.223 r_sphericity_free 1.836 r_scbond_it 1.817 r_mcangle_it 1.383 r_angle_refined_deg 1.203 r_rigid_bond_restr 0.895 r_mcbond_it 0.835 r_angle_other_deg 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.641 r_scangle_it 2.689 r_sphericity_bonded 2.223 r_sphericity_free 1.836 r_scbond_it 1.817 r_mcangle_it 1.383 r_angle_refined_deg 1.203 r_rigid_bond_restr 0.895 r_mcbond_it 0.835 r_angle_other_deg 0.825 r_symmetry_vdw_other 0.28 r_nbd_other 0.244 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.122 r_nbtor_other 0.084 r_chiral_restr 0.079 r_gen_planes_other 0.011 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3870 Nucleic Acid Atoms Solvent Atoms 950 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing