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Crystal structure of CERT START domain in complex with C10-diacylglycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.05 39.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.754 α = 90 b = 75.013 β = 107.92 c = 41.753 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 95 CCD ADSC QUANTUM 210 2007-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 Photon Factory AR-NW12A
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 1.8 50 99.4 0.058 5 21390 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.79 1.85 97.2 0.37 3.6 2058
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2E3N 1.8 39.72 20249 1093 98.7 0.23477 0.23296 0.2311 0.26723 0.2688 RANDOM 36.919
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.878 r_dihedral_angle_4_deg 18.784 r_dihedral_angle_3_deg 14.493 r_dihedral_angle_1_deg 6.739 r_scangle_it 3.691 r_scbond_it 2.315 r_mcangle_it 1.735 r_angle_refined_deg 1.421 r_mcbond_it 1.045 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.878 r_dihedral_angle_4_deg 18.784 r_dihedral_angle_3_deg 14.493 r_dihedral_angle_1_deg 6.739 r_scangle_it 3.691 r_scbond_it 2.315 r_mcangle_it 1.735 r_angle_refined_deg 1.421 r_mcbond_it 1.045 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 1852 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling XFIT data reduction