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The structure of EntE with 3-(prop-2-yn-1-yloxy)benzoic acid sulfamoyl adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 HEPES-Na, MPD
Crystal Properties Matthews coefficient Solvent content 2.48 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.041 α = 90 b = 57.649 β = 96.64 c = 171.427 γ = 90
Symmetry Space Group I 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 100 PIXEL DECTRIS PILATUS3 S 2M 2020-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.65 50 99.5 0.102 0.993 5.9 3.4 35229
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.8 99.1 0.468 0.832 1.9 3.5
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 2.65 45.56 33486 1742 99.37 0.1893 0.1877 0.1932 0.2192 0.2249 RANDOM 35.236
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] 1.4 1.06 -0.98 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.723 r_dihedral_angle_4_deg 19.119 r_dihedral_angle_3_deg 16.145 r_dihedral_angle_1_deg 7.037 r_angle_refined_deg 1.586 r_angle_other_deg 1.259 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.723 r_dihedral_angle_4_deg 19.119 r_dihedral_angle_3_deg 16.145 r_dihedral_angle_1_deg 7.037 r_angle_refined_deg 1.586 r_angle_other_deg 1.259 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8138 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing Coot model building