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Crystal structure of rabbit NOD2 in an ADP-bound state (Crystal form1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 5% PEG 20000, 5% MPD, 100 mM Hepes pH 7.8, 500 mM NaCl
Crystal Properties Matthews coefficient Solvent content 4.25 71.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.815 α = 90 b = 106.162 β = 90 c = 185.393 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 92.7 92.6 29.7 6.7 57510
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.34 92.7 57509 3063 91.77 0.20329 0.20155 0.2057 0.23585 0.2365 RANDOM 76.976
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] -0.02 -0.54 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.627 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 15.538 r_long_range_B_refined 10.265 r_long_range_B_other 10.264 r_scangle_other 8.058 r_mcangle_it 7.018 r_mcangle_other 7.017 r_dihedral_angle_1_deg 6.053 r_scbond_it 5.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.627 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 15.538 r_long_range_B_refined 10.265 r_long_range_B_other 10.264 r_scangle_other 8.058 r_mcangle_it 7.018 r_mcangle_other 7.017 r_dihedral_angle_1_deg 6.053 r_scbond_it 5.511 r_scbond_other 5.51 r_mcbond_it 5.01 r_mcbond_other 5.01 r_angle_refined_deg 1.507 r_angle_other_deg 0.992 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5833 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing