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Crystal structure of POFUT1 in complex with GDP-fucose (crystal-form-II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZY2 PDB ENTRY 3ZY2
Crystallization Crystal Properties Matthews coefficient Solvent content 2.29 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.583 α = 90 b = 38.156 β = 102.85 c = 68.101 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 90 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER ESRF BM16
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 1.91 20 98.9 0.1 9.27 4.37 39386 2
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 1.91 2.01 96.5 0.52 1.97 3.91
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 PDB ENTRY 3ZY2 1.91 70.48 27452 745 98.79 0.20314 0.2022 0.2019 0.23733 0.2387 RANDOM 26.879
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] -0.67 -1.79 1.25 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.13 r_dihedral_angle_3_deg 16.632 r_dihedral_angle_4_deg 15.612 r_dihedral_angle_1_deg 6.017 r_scangle_it 2.941 r_scbond_it 1.893 r_angle_refined_deg 1.375 r_mcangle_it 1.152 r_mcbond_it 0.643 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.13 r_dihedral_angle_3_deg 16.632 r_dihedral_angle_4_deg 15.612 r_dihedral_angle_1_deg 6.017 r_scangle_it 2.941 r_scbond_it 1.893 r_angle_refined_deg 1.375 r_mcangle_it 1.152 r_mcbond_it 0.643 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2794 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOLREP phasing