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Crystal structure of human AGX1 mutant complexed with UDPGLCNAC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.2 M MgCl2, 0.1 M Tris, pH 8.5, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.97 37.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.614 α = 95.63 b = 64.569 β = 101.09 c = 82.07 γ = 104.93
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 2018-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.976280 Diamond I24
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 1.7 79.56 96.5 0.043 0.051 0.027 0.999 16.4 3.5 93417
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 1.7 1.73 90.9 0.429 0.518 0.286 0.813 3.2
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 1JV1 1.7 29.26 88736 4676 96.54 0.189 0.1871 0.1965 0.226 0.1967 RANDOM 24.492
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] 1.01 0.59 -0.77 -0.59 -0.36 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.143 r_dihedral_angle_3_deg 16.299 r_dihedral_angle_4_deg 15.576 r_dihedral_angle_1_deg 5.96 r_angle_refined_deg 1.64 r_angle_other_deg 1.039 r_chiral_restr 0.192 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.143 r_dihedral_angle_3_deg 16.299 r_dihedral_angle_4_deg 15.576 r_dihedral_angle_1_deg 5.96 r_angle_refined_deg 1.64 r_angle_other_deg 1.039 r_chiral_restr 0.192 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7535 Nucleic Acid Atoms Solvent Atoms 701 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing