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Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 12:0 phosphatidic acid (12:0 PA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Human ceramide-1-phosphate transfer protein in complex with 2:0 Ceramide-1-phosphate (2:0 C1P)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M Sodium acetate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.91 α = 90 b = 78.116 β = 90 c = 107.707 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 CCD ADSC QUANTUM 315r 2010-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 50 99.5 0.058 10.8 5.9 31943 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 98.6 0.459 5.9 3092
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 THROUGHOUT Human ceramide-1-phosphate transfer protein in complex with 2:0 Ceramide-1-phosphate (2:0 C1P) 1.898 32.622 0.12 31035 1946 96.84 0.1913 0.1884 0.1868 0.2337 0.2308 Random 32.8411
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] 1.7804 -0.1928 -1.5876
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.317 f_angle_d 0.871 f_chiral_restr 0.058 f_plane_restr 0.009 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3284 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 80
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling