☰ Navigation Tabs
Crystal structure of Aspergillus fumigatus phosphoglucomutase in complex with the reaction intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 90 mM sodium fluoride, 90 mM sodium bromide, 90 mM sodium iodide, 100 mM Tris-bicine pH 8.5, 20% v/v polyethylene glycol 550 MME, 10 % w/v polyethylene glycol 20000
Crystal Properties Matthews coefficient Solvent content 2.59 52.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.57 α = 90 b = 209.61 β = 90 c = 61.2 γ = 90
Symmetry Space Group P 21 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 EIGER X 4M 2016-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
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 2.48 89.2 98.4 0.994 11.2 4.2 44960
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 2.48 2.53 0.795
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 5EPC 2.48 89.2 42710 2250 98.39 0.2041 0.2011 0.2063 0.2584 0.2597 RANDOM 37.597
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] -2.75 0.24 2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.691 r_dihedral_angle_4_deg 24.033 r_dihedral_angle_3_deg 18.859 r_dihedral_angle_1_deg 7.523 r_angle_refined_deg 1.629 r_angle_other_deg 1.272 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.691 r_dihedral_angle_4_deg 24.033 r_dihedral_angle_3_deg 18.859 r_dihedral_angle_1_deg 7.523 r_angle_refined_deg 1.629 r_angle_other_deg 1.272 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8545 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 42
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling