☰ Navigation Tabs
a glycosyltransferase complex with UDP and the product
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 2.32 47.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.662 α = 90 b = 97.662 β = 90 c = 89.626 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 2016-01-11 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) 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 1.7 42.88 100 0.084 0.088 0.027 18.9 19.1 54657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 1.139 1.201 0.38
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 1.7 42.88 51453 2725 99.13 0.16259 0.16115 0.175 0.19016 0.2041 RANDOM 31.239
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] -0.64 -0.32 -0.64 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.846 r_dihedral_angle_4_deg 16.749 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 6.874 r_long_range_B_other 6.148 r_long_range_B_refined 6.146 r_scangle_other 4.032 r_scbond_it 2.664 r_scbond_other 2.664 r_mcangle_other 2.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.846 r_dihedral_angle_4_deg 16.749 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 6.874 r_long_range_B_other 6.148 r_long_range_B_refined 6.146 r_scangle_other 4.032 r_scbond_it 2.664 r_scbond_other 2.664 r_mcangle_other 2.288 r_mcangle_it 2.287 r_angle_refined_deg 1.627 r_mcbond_it 1.544 r_mcbond_other 1.542 r_angle_other_deg 1.376 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 273 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing