2E3Q

Crystal structure of CERT START domain in complex with C18-ceramide (P212121)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2745.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.196α = 90
b = 54.783β = 90
c = 90.314γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.00000Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.085099.916553
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.082.1599.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0846.831565383599.80.1840.1820.237RANDOM28.96
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]
1.290.43-1.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.573
r_dihedral_angle_4_deg15.211
r_dihedral_angle_3_deg14.607
r_dihedral_angle_1_deg6.25
r_scangle_it4.476
r_scbond_it2.764
r_mcangle_it1.848
r_angle_refined_deg1.564
r_mcbond_it1.087
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.573
r_dihedral_angle_4_deg15.211
r_dihedral_angle_3_deg14.607
r_dihedral_angle_1_deg6.25
r_scangle_it4.476
r_scbond_it2.764
r_mcangle_it1.848
r_angle_refined_deg1.564
r_mcbond_it1.087
r_nbtor_refined0.308
r_nbd_refined0.208
r_symmetry_vdw_refined0.192
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.145
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1903
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms44

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling