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E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S F88Y in complex with spermidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.1 M Sodium acetate pH 4.6, 0.2 M Ammonium acetate, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.14 42.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.136 α = 90 b = 78.606 β = 90 c = 114.831 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2019-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.95 46.36 98.9 0.206 0.227 0.093 0.994 6.44 5.5 25021 30.12
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 1.95 2.02 99.2 2.231 2.451 0.996 0.262 0.79 5.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1A99 1.95 46.36 25007 1251 98.93 0.2029 0.2008 0.201 0.2418 0.2415 35.92
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.9189 f_angle_d 0.6791 f_chiral_restr 0.0499 f_bond_d 0.0047 f_plane_restr 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2687 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 55
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing