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E.coli's Putrescine receptor PotF in its open apo state
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 7.2 293 0.1 M Tris pH 7.2, 0.2 M NaCl, 35% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.12 41.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.22 α = 90 b = 53.45 β = 111.593 c = 88.13 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2018-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.18 45.9 99.95 0.1565 0.1642 0.04914 0.997 13.39 10.9 67443 29.95
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 2.18 2.258 99.91 0.9698 1.023 0.3195 0.871 4.65 9.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1A99 2.18 45.9 1.35 67443 3852 99.92 0.2303 0.2277 0.2284 0.273 0.2735 Random selection 43.22
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 16.5881 f_angle_d 0.4961 f_chiral_restr 0.0426 f_plane_restr 0.0034 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5360 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 115
Software Software Software Name Purpose MxCuBE data collection PHENIX refinement XDS data reduction XDS data scaling PHASER phasing XSCALE data scaling Coot model building