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Carbohydrate-binding of the starch binding domain of Rhizopus oryzae glucoamylase in complex with beta-cyclodextrin and maltoheptaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DJM PDB ENTRY 2DJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PEG8K, ZINC ACETATE, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.591 α = 90 b = 42.725 β = 90 c = 70.064 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 273 CCD ADSC CCD 2006-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 NSRRC BL13C1
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 1.8 30 99.1 0.03 41.3 4.4 12310 2 19.8
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 1.8 1.86 94.1 0.44 2.25
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 (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 2DJM 1.8 21.36 2 10806 552 87.3 0.222 0.222 0.2261 0.236 0.2375 RANDOM 31
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] -1.42 -0.89 2.31
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_angle_deg 1.3 c_improper_angle_d 0.85 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_angle_deg 1.3 c_improper_angle_d 0.85 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 827 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 78
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing