☰ Navigation Tabs
Structural studies of Phe256Trp of human salivary alpha-amylase: implications for the role of a conserved water molecule and its associated chain in enzyme activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MFV PDB ENTRY 1MFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 MPD, Calcium Chloride, Tris, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal Properties Matthews coefficient Solvent content 2.32 46.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.9 α = 90 b = 74.2 β = 90 c = 134.82 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 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2001-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 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 2.07 41.1 94.5 0.06 13 3 89732 30610 1 1 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.07 2.14 60
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MFV 2.07 41.17 30610 29010 1551 94.04 0.15874 0.15623 0.1695 0.20585 0.2172 RANDOM 24.753
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 6.949 r_scangle_it 3.477 r_scbond_it 2.225 r_angle_refined_deg 1.547 r_mcangle_it 1.432 r_angle_other_deg 0.92 r_mcbond_it 0.791 r_symmetry_vdw_other 0.299 r_nbd_other 0.246 r_nbd_refined 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.949 r_scangle_it 3.477 r_scbond_it 2.225 r_angle_refined_deg 1.547 r_mcangle_it 1.432 r_angle_other_deg 0.92 r_mcbond_it 0.791 r_symmetry_vdw_other 0.299 r_nbd_other 0.246 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.164 r_chiral_restr 0.098 r_nbtor_other 0.087 r_symmetry_vdw_refined 0.074 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3949 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement AMoRE phasing