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The structure of UDP-glucose pyrophosphorylase from Aspergillus fumigatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.8 M lithium sulphate monohydrate, and 0.1 M sodium acetate trihydrate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.99 69.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.16 α = 90 b = 152.61 β = 90 c = 160.01 γ = 90
Symmetry Space Group I 2 2 2
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-F 2015-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9281 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.57 80.01 99.9 0.99 15.2 6.5 52428
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.65 0.514
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 2I5K 2.57 80 49727 2699 99.8 0.2295 0.227 0.2305 0.2774 0.2792 RANDOM 68.311
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] -1.15 -0.03 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.558 r_dihedral_angle_3_deg 20.284 r_dihedral_angle_4_deg 18.512 r_dihedral_angle_1_deg 8.031 r_angle_refined_deg 1.641 r_angle_other_deg 1.204 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.558 r_dihedral_angle_3_deg 20.284 r_dihedral_angle_4_deg 18.512 r_dihedral_angle_1_deg 8.031 r_angle_refined_deg 1.641 r_angle_other_deg 1.204 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6903 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing