2E3O

Crystal structure of CERT START domain in complex with C16-ceramide (P212121)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.4549.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.958α = 90
b = 57.068β = 90
c = 88.661γ = 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-6A1.0000Photon 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
11.555099.141548
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.551.6195.1

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 REPLACEMENTTHROUGHOUT1.554839436211199.10.2010.20.218RANDOM19.94
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]
0.520.17-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.203
r_dihedral_angle_4_deg14.743
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg5.783
r_scangle_it2.81
r_scbond_it1.847
r_angle_refined_deg1.228
r_mcangle_it1.2
r_mcbond_it0.741
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.203
r_dihedral_angle_4_deg14.743
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg5.783
r_scangle_it2.81
r_scbond_it1.847
r_angle_refined_deg1.228
r_mcangle_it1.2
r_mcbond_it0.741
r_nbtor_refined0.305
r_nbd_refined0.201
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.167
r_symmetry_vdw_refined0.104
r_chiral_restr0.084
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms1956
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms46

Software

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