2Z9Y

Crystal structure of CERT START domain in complex with C10-diacylglycerol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E3N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPVAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.0539.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.754α = 90
b = 75.013β = 107.92
c = 41.753γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102007-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.85099.40.0585213901
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.791.8597.20.373.62058

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT2E3N1.839.7220249109398.70.234770.232960.26723RANDOM36.919
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]
1.1-1.42-0.66-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.878
r_dihedral_angle_4_deg18.784
r_dihedral_angle_3_deg14.493
r_dihedral_angle_1_deg6.739
r_scangle_it3.691
r_scbond_it2.315
r_mcangle_it1.735
r_angle_refined_deg1.421
r_mcbond_it1.045
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.878
r_dihedral_angle_4_deg18.784
r_dihedral_angle_3_deg14.493
r_dihedral_angle_1_deg6.739
r_scangle_it3.691
r_scbond_it2.315
r_mcangle_it1.735
r_angle_refined_deg1.421
r_mcbond_it1.045
r_nbtor_refined0.307
r_symmetry_vdw_refined0.225
r_nbd_refined0.208
r_xyhbond_nbd_refined0.127
r_symmetry_hbond_refined0.104
r_chiral_restr0.091
r_bond_refined_d0.013
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 Atoms1852
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
XFITdata reduction