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Crystal structure of a trafficking protein particle complex subunit 3 from Naegleria fowleri covalently bound to palmitic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SZ7 PDB entry 1SZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 22 mg/mL NafoA.00964.a.B1 PS38152 against JCSG+ screen condition H10 (0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350), cryoprotectant: 15% ethylene glycol, crystal tracking ID 288103h10, unique puck ID afj8-5
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.64 α = 114.55 b = 78.67 β = 87.67 c = 80.57 γ = 95.02
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2017-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.4 33.381 98.1 0.043 0.05 0.999 18.62 3.868 45852 -3 53.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 97.6 0.55 0.636 0.828 2.75 3.975
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1SZ7 2.4 33.381 1.99 45811 2024 98.22 0.173 0.1712 0.1764 0.2086 0.2125 67.4393
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 15.402 f_angle_d 0.92 f_chiral_restr 0.055 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7715 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 146
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing