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A glycosyltransferase with UDP and the substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M sodium citrate buffer at pH 5.4 and 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.553 α = 90 b = 97.553 β = 90 c = 90.774 γ = 120
Symmetry Space Group P 31 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 PILATUS 6M 2017-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978 SSRF BL19U1
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 2.1 84.46 100 0.127 0.158 0.091 0.973 7.2 5.3 29548
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 2.1 2.15 0.29 0.361 0.212 0.916
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PQ6 2.1 61.84 29548 2267 99.63 0.16859 0.16706 0.1617 0.19778 0.1866 RANDOM 38.764
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] -0.68 -0.34 -0.68 2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.815 r_dihedral_angle_4_deg 15.097 r_dihedral_angle_3_deg 12.07 r_long_range_B_refined 7.288 r_long_range_B_other 7.287 r_dihedral_angle_1_deg 6.137 r_scangle_other 5.381 r_scbond_it 3.664 r_scbond_other 3.663 r_mcangle_it 3.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.815 r_dihedral_angle_4_deg 15.097 r_dihedral_angle_3_deg 12.07 r_long_range_B_refined 7.288 r_long_range_B_other 7.287 r_dihedral_angle_1_deg 6.137 r_scangle_other 5.381 r_scbond_it 3.664 r_scbond_other 3.663 r_mcangle_it 3.654 r_mcangle_other 3.654 r_mcbond_it 2.516 r_mcbond_other 2.516 r_angle_refined_deg 1.44 r_angle_other_deg 0.93 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3607 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing