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Probing the role of a mobile loop in human salivary amylase: Structural studies on the loop-deleted mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JXK PDB entry 1jxk
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 soaking with acarbose at 1 mM concentration for 24 hours 9 298 40% mpd, pH 9.0, soaking with acarbose at 1 mM concentration for 24 hours, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.074 α = 90 b = 73.815 β = 90 c = 135.787 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 26.54 96.8 0.06 0.06 24.5 4.8 35031 35031 1 1 25.6
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 0.267 0.267 7 3488
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 1jxk 2 26.54 35031 33226 1746 96.86 0.1622 0.16226 0.16011 0.1638 0.20109 0.2082 RANDOM 25.789
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 6.254 r_scangle_it 2.997 r_scbond_it 2.041 r_angle_refined_deg 1.368 r_mcangle_it 1.265 r_mcbond_it 0.691 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.254 r_scangle_it 2.997 r_scbond_it 2.041 r_angle_refined_deg 1.368 r_mcangle_it 1.265 r_mcbond_it 0.691 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.096 r_metal_ion_refined 0.077 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3924 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 199
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement