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Glycosidase F290Y at pH8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.2 M Ammonium citrate (pH 8.0), 8% PEG monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.8 56.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.806 α = 90 b = 104.806 β = 90 c = 89.819 γ = 90
Symmetry Space Group P 4 21 2
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 2M 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.71 41.59 99.9 0.222 0.226 0.999 0.134 26.1 54864
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.81 99.7 4.575 4.667 0.529 0.0084 25.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5Z3D 1.71 41.59 54862 2740 99.893 0.165 0.1633 0.1741 0.1894 0.1963 27.482
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] 0.489 0.489 -0.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.326 r_dihedral_angle_4_deg 20.009 r_dihedral_angle_3_deg 12.412 r_dihedral_angle_1_deg 5.998 r_lrange_it 5.753 r_lrange_other 5.5 r_scangle_it 4.303 r_scangle_other 4.302 r_scbond_other 3.047 r_scbond_it 3.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.326 r_dihedral_angle_4_deg 20.009 r_dihedral_angle_3_deg 12.412 r_dihedral_angle_1_deg 5.998 r_lrange_it 5.753 r_lrange_other 5.5 r_scangle_it 4.303 r_scangle_other 4.302 r_scbond_other 3.047 r_scbond_it 3.046 r_mcangle_other 2.962 r_mcangle_it 2.955 r_mcbond_it 2.264 r_mcbond_other 2.232 r_angle_refined_deg 1.65 r_angle_other_deg 1.548 r_symmetry_nbd_refined 0.309 r_nbd_other 0.244 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.193 r_chiral_restr_other 0.186 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.151 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2865 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing