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Crystal structure of the human NLRP9 pyrin domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 20%(w/v) PEG MME 2,000
0.1M Tris pH 8.5
0.2M Trimethylamine n-oxide
Crystal Properties Matthews coefficient Solvent content 1.66 25.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.97 α = 90 b = 33.685 β = 102.397 c = 49.667 γ = 90
Symmetry Space Group C 1 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 125 PIXEL DECTRIS EIGER2 X 9M 2019-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.000 PAL/PLS 5C (4A)
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 2.08 28.08 98.9 0.073 22.28 6.2 5035
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 2.1 2.15 0.533
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4EWI 2.08 28.08 5035 272 97.748 0.217 0.2133 0.2179 0.2825 0.2743 39.069
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] -1.624 2.149 -0.397 0.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.122 r_dihedral_angle_3_deg 18.71 r_dihedral_angle_4_deg 7.648 r_lrange_other 7.029 r_lrange_it 7.009 r_scangle_it 6.485 r_scangle_other 6.48 r_dihedral_angle_1_deg 5.555 r_scbond_it 5.159 r_scbond_other 5.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.122 r_dihedral_angle_3_deg 18.71 r_dihedral_angle_4_deg 7.648 r_lrange_other 7.029 r_lrange_it 7.009 r_scangle_it 6.485 r_scangle_other 6.48 r_dihedral_angle_1_deg 5.555 r_scbond_it 5.159 r_scbond_other 5.153 r_mcangle_other 4.956 r_mcangle_it 4.923 r_mcbond_it 4.098 r_mcbond_other 4.038 r_angle_other_deg 2.104 r_angle_refined_deg 1.754 r_nbd_other 0.314 r_symmetry_nbd_other 0.243 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.227 r_nbtor_refined 0.199 r_symmetry_nbd_refined 0.164 r_chiral_restr 0.114 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_refined 0.035 r_bond_other_d 0.032 r_bond_refined_d 0.015 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_symmetry_xyhbond_nbd_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 786 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing