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Sucrose phosphorylase from Faecalibaculum rodentium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 Protein was concentrated to 30 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 1 M Na citrate, 0.1 M Tris, pH 7.0, 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 1.95 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.798 α = 90 b = 94.409 β = 90 c = 104.772 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 PIXEL DECTRIS PILATUS3 2M 2020-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.36 46 99.7 0.076 0.095 0.056 0.999 10.7 5 95834
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.38 1.27 1.583 0.933 0.45 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 6S9V 1.36 46 95748 4844 99.564 0.151 0.1495 0.1488 0.1853 0.185 16.554
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] -0.567 -1.915 2.483
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.472 r_dihedral_angle_4_deg 14.923 r_dihedral_angle_3_deg 11.739 r_rigid_bond_restr 7.317 r_dihedral_angle_1_deg 6.556 r_lrange_it 3.062 r_lrange_other 2.805 r_scangle_it 2.46 r_scangle_other 2.46 r_scbond_it 2.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.472 r_dihedral_angle_4_deg 14.923 r_dihedral_angle_3_deg 11.739 r_rigid_bond_restr 7.317 r_dihedral_angle_1_deg 6.556 r_lrange_it 3.062 r_lrange_other 2.805 r_scangle_it 2.46 r_scangle_other 2.46 r_scbond_it 2.036 r_scbond_other 2.035 r_mcangle_other 1.714 r_mcangle_it 1.711 r_angle_other_deg 1.421 r_mcbond_it 1.372 r_angle_refined_deg 1.364 r_mcbond_other 1.357 r_nbd_refined 0.21 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.173 r_nbd_other 0.17 r_symmetry_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_other 0.079 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3918 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 8
Software Software Software Name Purpose XDS data scaling Aimless data scaling PHASER phasing REFMAC refinement