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Crystal structure of Caspace Activation and Recruitment Domain (CARD) of NOD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.7 277 15% PEG 3000, 100mM acetate, 20mgs/ml protein, pH 4.7, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.76 55.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.141 α = 90 b = 40.141 β = 90 c = 150.748 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 CCD MAR CCD 165 mm 2006-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.979 APS 23-ID-B
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 2 28.38 99.3 0.059 21.3 13.26 9009 8946 1 1 47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.5 0.355 4.8 13.13 862
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1DGN 2 10.78 9009 8874 418 99.38 0.222 0.221 0.2341 0.262 0.2734 RANDOM 63.506
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] 1.75 1.75 -3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.688 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 15.652 r_dihedral_angle_1_deg 6.055 r_scangle_it 2.343 r_scbond_it 1.68 r_angle_refined_deg 1.34 r_angle_other_deg 0.997 r_mcangle_it 0.991 r_mcbond_it 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.688 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 15.652 r_dihedral_angle_1_deg 6.055 r_scangle_it 2.343 r_scbond_it 1.68 r_angle_refined_deg 1.34 r_angle_other_deg 0.997 r_mcangle_it 0.991 r_mcbond_it 0.872 r_symmetry_vdw_other 0.228 r_nbd_refined 0.215 r_nbtor_refined 0.173 r_nbd_other 0.163 r_mcbond_other 0.15 r_xyhbond_nbd_refined 0.131 r_nbtor_other 0.093 r_chiral_restr 0.09 r_symmetry_hbond_refined 0.083 r_symmetry_vdw_refined 0.081 r_bond_refined_d 0.012 r_bond_other_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 771 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection d*TREK data reduction PHASER phasing