2E3R

Crystal structure of CERT START domain in complex with C18-ceramide (P1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3246.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.459α = 77.54
b = 50.134β = 70.96
c = 62.652γ = 81.85
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.97919Photon FactoryAR-NW12A

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
11.6558.2295.559501
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.651.7190.1

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 REPLACEMENTTHROUGHOUT1.655056486301595.20.1940.1920.226RANDOM23.08
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]
0.150.490.03-0.010.19-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.028
r_dihedral_angle_4_deg17.824
r_dihedral_angle_3_deg13.917
r_dihedral_angle_1_deg5.73
r_scangle_it3.74
r_scbond_it2.301
r_mcangle_it1.45
r_angle_refined_deg1.325
r_mcbond_it0.871
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.028
r_dihedral_angle_4_deg17.824
r_dihedral_angle_3_deg13.917
r_dihedral_angle_1_deg5.73
r_scangle_it3.74
r_scbond_it2.301
r_mcangle_it1.45
r_angle_refined_deg1.325
r_mcbond_it0.871
r_nbtor_refined0.306
r_nbd_refined0.202
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.162
r_symmetry_vdw_refined0.131
r_chiral_restr0.094
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms3754
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms80

Software

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