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Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 18:1 Ceramide-1-Phosphate (18:1-C1P)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other CPTP in complex with 2:0 ceramide-1-phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M Sodium malonate, 0.1 M Bis-Tris Propane pH 6.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.46 64.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 236.983 α = 90 b = 128.758 β = 93.53 c = 66.663 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 CCD ADSC QUANTUM 315r 2010-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C
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 3.1 30 99.3 0.11 8.3 4.9 35765
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 3.1 3.21 98 0.478 5
Refinement Statistics Diffraction ID Structure Solution 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 CPTP in complex with 2:0 ceramide-1-phosphate 3.102 30.052 1.35 35733 1784 98.52 0.2271 0.225 0.2308 0.2633 0.2667 89.3277
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] -11.1732 2.4873 10.6599 0.5133
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.556 f_angle_d 0.872 f_chiral_restr 0.058 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9865 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 219
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction