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Glycosidase F290Y at pH4.5
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 7 293 0.2 M Ammonium citrate (pH 7.0), 8% PEG monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.811 α = 90 b = 104.811 β = 90 c = 90.158 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 1.91 46.92 99.9 0.238 0.242 0.998 0.107 26.4 39724
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 1.91 2.02 99.8 3.651 3.722 0.429 0.01 26.7
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 1.91 46.92 39723 1992 99.942 0.183 0.1819 0.191 0.2117 0.2197 36.2
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] 0.143 0.143 -0.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.762 r_dihedral_angle_4_deg 20.088 r_dihedral_angle_3_deg 13.339 r_lrange_it 6.485 r_lrange_other 6.334 r_dihedral_angle_1_deg 6.017 r_scangle_it 4.903 r_scangle_other 4.902 r_mcangle_other 3.787 r_mcangle_it 3.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.762 r_dihedral_angle_4_deg 20.088 r_dihedral_angle_3_deg 13.339 r_lrange_it 6.485 r_lrange_other 6.334 r_dihedral_angle_1_deg 6.017 r_scangle_it 4.903 r_scangle_other 4.902 r_mcangle_other 3.787 r_mcangle_it 3.783 r_scbond_it 3.461 r_scbond_other 3.448 r_mcbond_it 2.863 r_mcbond_other 2.846 r_angle_refined_deg 1.623 r_angle_other_deg 1.449 r_symmetry_xyhbond_nbd_refined 0.227 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.182 r_nbd_other 0.182 r_chiral_restr_other 0.175 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.136 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.079 r_xyhbond_nbd_other 0.013 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 276 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing