☰ Navigation Tabs
a glycosyltransferase complex with UDP
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 2015-12-14 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 1.69 49.58 100 0.069 0.072 0.022 0.999 20.2 19.2 56938
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 1.69 1.73 1.007 1.061 0.333 0.948 4
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 1.69 48.83 53830 2853 97.48 0.1797 0.1782 0.1857 0.20744 0.2094 RANDOM 38.083
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] -0.01 -0.01 -0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.833 r_dihedral_angle_4_deg 17.22 r_dihedral_angle_3_deg 13.189 r_dihedral_angle_1_deg 6.544 r_long_range_B_refined 5.881 r_long_range_B_other 5.867 r_scangle_other 3.2 r_mcangle_it 2.492 r_mcangle_other 2.491 r_scbond_it 2.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.833 r_dihedral_angle_4_deg 17.22 r_dihedral_angle_3_deg 13.189 r_dihedral_angle_1_deg 6.544 r_long_range_B_refined 5.881 r_long_range_B_other 5.867 r_scangle_other 3.2 r_mcangle_it 2.492 r_mcangle_other 2.491 r_scbond_it 2.008 r_scbond_other 2.007 r_mcbond_it 1.605 r_mcbond_other 1.602 r_angle_refined_deg 1.489 r_angle_other_deg 0.951 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3582 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing