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The structure of Aspergillus fumigatus phosphoglucose isomerase in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1.4 M citrate, 0.1 M Hepes-NaOH pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.41 63.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.651 α = 90 b = 84.651 β = 90 c = 232.501 γ = 90
Symmetry Space Group P 43 21 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 EIGER2 XE 16M 2023-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.12 29.93 99.7 1 33.2 26.3 49009
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 2.12 2.18 0.989
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.12 29.7 46393 2520 99.69 0.17375 0.17144 0.1816 0.21716 0.222 RANDOM 49.152
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] 2.97 2.97 -5.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.947 r_dihedral_angle_2_deg 7.852 r_long_range_B_refined 7.067 r_long_range_B_other 7.052 r_dihedral_angle_1_deg 6.565 r_scangle_other 6.077 r_mcangle_it 4.925 r_mcangle_other 4.924 r_scbond_it 4.622 r_scbond_other 4.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.947 r_dihedral_angle_2_deg 7.852 r_long_range_B_refined 7.067 r_long_range_B_other 7.052 r_dihedral_angle_1_deg 6.565 r_scangle_other 6.077 r_mcangle_it 4.925 r_mcangle_other 4.924 r_scbond_it 4.622 r_scbond_other 4.621 r_mcbond_it 4.015 r_mcbond_other 4.013 r_angle_refined_deg 1.488 r_angle_other_deg 0.522 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4300 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction pointless data scaling