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X-ray crystal structure of the E249Q mutant of alpha-amylase I from Eisenia fetida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M4K
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 sulfate, 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.83 56.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.897 α = 90 b = 96.897 β = 90 c = 121.957 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 EIGER X 16M 2018-11-23 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 1.6 49.33 100 0.05 0.058 0.999 20.1 7.9 87577 19.8550860307
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 1.6 1.63 99.6 0.528 0.609 0.897 3.5 7.8
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 6M4K 1.6 41.958 1.33473009263 87523 4353 99.9474699951 0.168807930266 0.167694673064 0.1686 0.190331477853 0.1918 23.2213397278
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 11.0717579777 f_angle_d 0.837040291568 f_chiral_restr 0.053588863238 f_plane_restr 0.0061971743403 f_bond_d 0.00603630103567
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3906 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 81
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing