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Crystal structure of rabbit NOD2 in an ADP-bound state (Crystal form2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277 5% PEG 10000, 100 mM Hepes pH 7.8, 500 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.4 63.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.153 α = 90 b = 122.87 β = 90 c = 177.555 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 CCD RAYONIX MX225HE 2014-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 SPring-8 BL32XU
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 3.3 50 100 8.4 6.1 35238
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 3.31 50 35238 1853 99.42 0.19511 0.19293 0.23681 0.2062 RANDOM 78.991
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] 0.05 0.3 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.225 r_dihedral_angle_4_deg 16.032 r_dihedral_angle_3_deg 15.749 r_long_range_B_refined 11.399 r_long_range_B_other 11.399 r_scangle_other 6.815 r_mcangle_it 6.349 r_mcangle_other 6.349 r_dihedral_angle_1_deg 5.168 r_scbond_it 4.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.225 r_dihedral_angle_4_deg 16.032 r_dihedral_angle_3_deg 15.749 r_long_range_B_refined 11.399 r_long_range_B_other 11.399 r_scangle_other 6.815 r_mcangle_it 6.349 r_mcangle_other 6.349 r_dihedral_angle_1_deg 5.168 r_scbond_it 4.149 r_scbond_other 4.149 r_mcbond_it 3.975 r_mcbond_other 3.973 r_angle_refined_deg 1.279 r_angle_other_deg 1.184 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 11987 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing