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Crystal structure of the PKD1 domain of Vibrio anguillarum Epp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 21mg/ml protein in 10 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM DTT was mixed with 0.1 M sodium cacodylate pH 6.5, 18% PEG8000 (w/v), 0.2 M zinc acetate in 1:1 volume ratio
Crystal Properties Matthews coefficient Solvent content 1.84 33.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.096 α = 90 b = 46.069 β = 97.39 c = 41.616 γ = 90
Symmetry Space Group C 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 6M 2017-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978530 SSRF BL19U1
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 1.272 38.566 96.7 0.065 0.07 0.027 0.999 19.3 6.7 33927 13.1
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 1.272 1.277 85.3 0.924 1.001 0.381 0.771 2.1 6.8
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 4L9D 1.272 35.253 1.35 33921 1705 96.7 0.1526 0.1508 0.1624 0.1862 0.1944 random 18
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 16.914 f_angle_d 1.147 f_chiral_restr 0.086 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1292 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing