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The apo structure of beta-1,2-glucosyltransferase from Ignavibacterium album
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M Tris-HCl (pH 7.5), 0.2M calcium acetate, 20%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.649 α = 90 b = 71.68 β = 105.39 c = 129.98 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 210 2016-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 65.33 99.4 0.038 17.7 3.1 146514
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 97.7 0.156 6 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 65.329 146292 7304 99.376 0.164 0.1619 0.1736 0.1973 0.2039 14.393
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] 0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.459 r_dihedral_angle_4_deg 19.935 r_dihedral_angle_3_deg 14.065 r_dihedral_angle_1_deg 6.974 r_lrange_it 4.461 r_lrange_other 4.437 r_scangle_it 3.529 r_scangle_other 3.529 r_scbond_it 2.261 r_scbond_other 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.459 r_dihedral_angle_4_deg 19.935 r_dihedral_angle_3_deg 14.065 r_dihedral_angle_1_deg 6.974 r_lrange_it 4.461 r_lrange_other 4.437 r_scangle_it 3.529 r_scangle_other 3.529 r_scbond_it 2.261 r_scbond_other 2.26 r_mcangle_it 2.094 r_mcangle_other 2.094 r_angle_refined_deg 1.681 r_angle_other_deg 1.453 r_mcbond_it 1.403 r_mcbond_other 1.402 r_nbd_refined 0.211 r_nbd_other 0.201 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.175 r_symmetry_nbd_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.142 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_symmetry_xyhbond_nbd_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11651 Nucleic Acid Atoms Solvent Atoms 729 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing