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Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 12:0 Ceramide-1-Phosphate (12:0-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 7 293 0.2 M Ammonium chloride, 0.1 M Hepes pH 7.0, 20% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.191 α = 90 b = 132.677 β = 96.98 c = 62.107 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 CCD ADSC QUANTUM 315 2009-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0750 NSLS X29A
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 99.1 0.072 9.8 5.5 70265
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 93.1 0.44 4.7
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 1.901 31.232 0.14 67553 3402 95.33 0.1837 0.1813 0.1803 0.2301 0.2264
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] -4.3866 -2.4213 10.0523 -5.6656
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.772 f_angle_d 0.971 f_chiral_restr 0.062 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6650 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 152
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction