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PanDDA analysis group deposition of ground-state model of INTERLEUKIN-1 BETA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NVH 2NVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 291 2.8M ammonium sulphate, 0.1M Tris pH7.9
Crystal Properties Matthews coefficient Solvent content 3.25 62.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.572 α = 90 b = 54.572 β = 90 c = 75.836 γ = 90
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 2019-07-23 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96871 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.27 54.57 100 0.041 0.044 0.017 0.999 17.6 6.5 58910
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.34 100 1.622 1.783 0.734 0.395 5.9 8591
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2NVH 1.27 54.63 55824 2883 99.65 0.1881 0.1873 0.197 0.2026 0.2109 RANDOM 22.439
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] 0.04 0.04 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.654 r_dihedral_angle_3_deg 12.552 r_dihedral_angle_1_deg 8.432 r_dihedral_angle_4_deg 7.617 r_mcangle_it 3.018 r_angle_refined_deg 2.008 r_mcbond_it 2.003 r_mcbond_other 1.985 r_angle_other_deg 1.87 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.654 r_dihedral_angle_3_deg 12.552 r_dihedral_angle_1_deg 8.432 r_dihedral_angle_4_deg 7.617 r_mcangle_it 3.018 r_angle_refined_deg 2.008 r_mcbond_it 2.003 r_mcbond_other 1.985 r_angle_other_deg 1.87 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1190 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing