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Ligand binding domain of the P. Putida receptor McpH in complex with Uric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold The initial model was generated with AlfaFold AF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293.5 100 mM cacodilato sodico a diferentes pH5.0, 30% Peg 8000,10% Glicerol,20 mM AcNA
Crystal Properties Matthews coefficient Solvent content 1.83 32.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.581 α = 90 b = 124.322 β = 99.33 c = 57.201 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 2016-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
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 1.95 124.32 96.1 0.055 0.068 0.039 0.998 11.4 2.9 31404
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 99.6 0.78 0.948 0.532 0.602 3.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AF2 1.95 32.15 1.34 31365 1581 96.03 0.1847 0.1822 0.231 0.2357
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 5.629 f_angle_d 1.005 f_chiral_restr 0.06 f_plane_restr 0.009 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3854 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 24
Software Software Software Name Purpose Aimless data scaling XDS data reduction PHENIX refinement REFMAC refinement MOLREP phasing