☰ Navigation Tabs
X-ray crystal structure of wild type alpha-amylase I from Eisenia fetida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KXQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 1.3 M lithium sulfate, 3% (v/v) PEG 400, 0.1 M magnesium chloride, 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.79 55.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.245 α = 90 b = 96.245 β = 90 c = 121.98 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2016-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.3 49.2203 100 0.05 0.056 0.999 20.2 9.9 160191 16.5515777525
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 100 0.858 0.965 0.847 2.6 9.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1KXQ 1.3 49.22 1.33016062502 160110 8087 99.9825150807 0.167933873213 0.167132596014 0.1677 0.183266623059 0.1841 20.1494242133
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 f_dihedral_angle_d 13.6729028366 f_angle_d 0.856266045877 f_chiral_restr 0.0821277962344 f_plane_restr 0.00624410812954 f_bond_d 0.00545062050489
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3909 Nucleic Acid Atoms Solvent Atoms 733 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing