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Role of mobile loop in the mechanism of human salivary 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 MPD, calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.24 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.295 α = 90 b = 75.25 β = 90 c = 135.018 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 200 IMAGE PLATE RIGAKU RAXIS IV mirrors 2001-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.99 65.94 97.7 0.062 0.051 16.2 3.2 36288 34452 2 23
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) 1.99 2.07 95 0.062 0.281 3
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 1.99 65.94 34452 34452 1795 97.7 0.1661 0.16615 0.16448 0.1688 0.19835 0.2016 RANDOM 22.987
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 4.826 r_scangle_it 3.419 r_scbond_it 2.299 r_angle_refined_deg 1.617 r_mcangle_it 1.412 r_mcbond_it 0.798 r_xyhbond_nbd_refined 0.22 r_chiral_restr 0.129 r_dihedral_angle_3_deg 0.129 r_xyhbond_nbd_other 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.826 r_scangle_it 3.419 r_scbond_it 2.299 r_angle_refined_deg 1.617 r_mcangle_it 1.412 r_mcbond_it 0.798 r_xyhbond_nbd_refined 0.22 r_chiral_restr 0.129 r_dihedral_angle_3_deg 0.129 r_xyhbond_nbd_other 0.123 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_nbtor_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3940 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 2
Software Software Software Name Purpose SCALEPACK data scaling AMoRE phasing REFMAC refinement