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Structure of the catalytic domain of Aspergillus niger Glucoamylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AGM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 PEG 3350, Hepes
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.369 α = 90 b = 73.125 β = 90 c = 102.88 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 CCD ADSC QUANTUM 210 2009-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.3 60 99.5 0.19 6.3 7.1 19454
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 1.516
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 1agm 2.3 59.67 18436 972 99.43 0.2555 0.2509 0.2536 0.3433 0.3442 RANDOM 56.096
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] 4.22 -8.09 3.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.944 r_dihedral_angle_3_deg 15.544 r_dihedral_angle_4_deg 14.228 r_dihedral_angle_1_deg 6.381 r_angle_other_deg 3.984 r_mcangle_it 3.808 r_mcbond_it 2.387 r_mcbond_other 2.378 r_angle_refined_deg 1.267 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.944 r_dihedral_angle_3_deg 15.544 r_dihedral_angle_4_deg 14.228 r_dihedral_angle_1_deg 6.381 r_angle_other_deg 3.984 r_mcangle_it 3.808 r_mcbond_it 2.387 r_mcbond_other 2.378 r_angle_refined_deg 1.267 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3542 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing