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Covalent intermediate in amylomaltase in complex with the acceptor analog 4-deoxyglucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OWC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.4-0.8 M sodium malonate pH 5.6, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.3 62.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.463 α = 90 b = 92.463 β = 90 c = 154.172 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAC Science DIP-2030 Osmic mirrors 2003-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
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 2.2 30 98.5 0.13 15 36721
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 2.2 2.28 98.3 0.59 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT 2OWC 2.2 14.94 36711 36711 1948 98.66 0.20019 0.19809 0.1979 0.23968 0.2379 RANDOM 29.137
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.179 r_dihedral_angle_4_deg 16.719 r_dihedral_angle_3_deg 16.567 r_dihedral_angle_1_deg 5.364 r_scangle_it 1.836 r_angle_refined_deg 1.291 r_scbond_it 1.152 r_mcangle_it 0.96 r_mcbond_it 0.527 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.179 r_dihedral_angle_4_deg 16.719 r_dihedral_angle_3_deg 16.567 r_dihedral_angle_1_deg 5.364 r_scangle_it 1.836 r_angle_refined_deg 1.291 r_scbond_it 1.152 r_mcangle_it 0.96 r_mcbond_it 0.527 r_nbtor_refined 0.313 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.064 r_gen_planes_refined 0.024 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4061 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement DIP data collection DENZO data reduction SCALEPACK data scaling