☰ Navigation Tabs
Crystal structure of rabbit NOD2 SER mutant in an ADP-bound state
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277 5% PEG 20000, 5% MPD, 100 mM Hepes pH 7.8, 500 mM NaCl
Crystal Properties Matthews coefficient Solvent content 4.24 71.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.9 α = 90 b = 107.845 β = 90 c = 185.365 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 2014-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 0.979 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 3.09 93.22 98.8 12.7 4.1 27203
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 3.09 93.22 27203 1457 98.11 0.20113 0.1985 0.2012 0.25026 0.2508 RANDOM 68.592
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] -3.71 9.45 -5.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.504 r_dihedral_angle_4_deg 18.249 r_dihedral_angle_3_deg 17.378 r_long_range_B_refined 9.2 r_long_range_B_other 9.199 r_scangle_other 6.396 r_dihedral_angle_1_deg 6.386 r_mcangle_it 6.267 r_mcangle_other 6.266 r_mcbond_it 3.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.504 r_dihedral_angle_4_deg 18.249 r_dihedral_angle_3_deg 17.378 r_long_range_B_refined 9.2 r_long_range_B_other 9.199 r_scangle_other 6.396 r_dihedral_angle_1_deg 6.386 r_mcangle_it 6.267 r_mcangle_other 6.266 r_mcbond_it 3.902 r_mcbond_other 3.902 r_scbond_it 3.815 r_scbond_other 3.815 r_angle_refined_deg 1.368 r_angle_other_deg 0.78 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 5792 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing