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Probing the role of a mobile loop in human slaivary amylase: Structural studies on the loop-deleted enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SMD pdb code 1smd
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 vapordiffusion, combined with soaking with inhibitor at 1 mM concentration 9 298 40% MPD, pH 9.0, vapordiffusion, combined with soaking with inhibitor at 1 mM concentration, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.681 α = 90 b = 73.197 β = 90 c = 134.448 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 4 monochromator 2002-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 20 96.7 0.091 0.091 32 5.4 34179 34179 1 1 28.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 98.9 0.37 0.37 5.8
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 (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 code 1smd 2 20 34179 31608 1660 94.48 0.1685 0.16854 0.16709 0.1708 0.19489 0.1984 RANDOM 28.086
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.248 r_scangle_it 2.966 r_scbond_it 2.003 r_angle_refined_deg 1.317 r_mcangle_it 1.221 r_mcbond_it 0.661 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.248 r_scangle_it 2.966 r_scbond_it 2.003 r_angle_refined_deg 1.317 r_mcangle_it 1.221 r_mcbond_it 0.661 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.096 r_metal_ion_refined 0.02 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3946 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 100
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement