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NOD1 card domain with three disulfide-clinched, domain-swapped dimers in the asymmetric unit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NZ7 PDB ENTRY 2NZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 288 2.07 M AMMONIUM CITRATE (DIBASIC), 6.7% (W/V) PEG3350, 10 mM TRIS-HCL FINAL PH ~5.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.01 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.846 α = 90 b = 85.335 β = 90 c = 113.682 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 ADSC QUANTUM 210 2011-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9770 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.15 25 75.9 0.084 9.66 3.6 34341 34341 -3 39.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 7 0.545 0.79 1.3
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 PDB ENTRY 2NZ7 2.15 24.84 34213 34213 1701 76.8 0.245 0.245 0.2438 0.275 0.2705 RANDOM 51.7
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] 1.52 -2.56 1.03
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.9 c_scangle_it 3.4 c_mcangle_it 2.37 c_scbond_it 2.25 c_mcbond_it 1.42 c_angle_deg 1.2 c_improper_angle_d 0.84 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.9 c_scangle_it 3.4 c_mcangle_it 2.37 c_scbond_it 2.25 c_mcbond_it 1.42 c_angle_deg 1.2 c_improper_angle_d 0.84 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4540 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 13
Software Software Software Name Purpose ADSC data collection PHASER phasing CNS refinement DENZO data reduction SCALEPACK data scaling