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Crystal Structure Analysis of Caspase-recruitment Domain (CARD) of Nod1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 20 % PEG 6000, 0.067 M MES (pH 6.0), 0.1 M diammonium hydrogen citrate, 0.09 M NaI, 0.001 M DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.21 61.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.091 α = 90 b = 79.091 β = 90 c = 80.863 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2006-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.977 CHESS F2
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 1.823 68.519 0.076 26.4 10.4 26612 26612 25.7
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) 1.823 0.516 4.6 9.8 2617
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MIR THROUGHOUT 1.9 35.53 23436 23436 1187 100 0.222 0.222 0.22 0.2391 0.266 0.2789 RANDOM 27.17
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.166 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_4_deg 12.78 r_sphericity_free 7.478 r_dihedral_angle_1_deg 5.873 r_scangle_it 4.533 r_sphericity_bonded 3.392 r_scbond_it 3.209 r_mcangle_it 2.531 r_rigid_bond_restr 2.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.166 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_4_deg 12.78 r_sphericity_free 7.478 r_dihedral_angle_1_deg 5.873 r_scangle_it 4.533 r_sphericity_bonded 3.392 r_scbond_it 3.209 r_mcangle_it 2.531 r_rigid_bond_restr 2.414 r_mcbond_it 1.695 r_angle_refined_deg 1.672 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.285 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1554 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction HKL-2000 data scaling