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Role of aromatic residues in human salivary alpha-amylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SMD PDB entry 1SMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 298 45% MPD, 0.1M Tris.HCl, 10 mM calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.085 α = 90 b = 74.873 β = 90 c = 134.69 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 77 CCD ADSC QUANTUM 4 mirrors 2007-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9777 CHESS A1
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 1.6 50 96.2 0.093 0.093 20.6 3.3 67719 64253 32
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) 1 1.6 1.63 92.7 0.439 0.439 2 2.1 3224
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 entry 1SMD 1.6 30.96 67719 64253 3405 96.25 0.195 0.18202 0.18075 0.1789 0.20532 0.203 RANDOM 23.671
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 0.42 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.695 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 12.279 r_dihedral_angle_1_deg 5.96 r_scangle_it 2.917 r_scbond_it 1.981 r_angle_refined_deg 1.352 r_mcangle_it 1.29 r_mcbond_it 0.822 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.695 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 12.279 r_dihedral_angle_1_deg 5.96 r_scangle_it 2.917 r_scbond_it 1.981 r_angle_refined_deg 1.352 r_mcangle_it 1.29 r_mcbond_it 0.822 r_nbtor_refined 0.314 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.158 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.097 r_metal_ion_refined 0.057 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3937 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing