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PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z355728146 in complex with 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 3.23 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.6 α = 90 b = 54.6 β = 90 c = 75.3 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 PILATUS 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 1.62 44.2 100 0.079 0.085 0.033 0.998 13.1 6.6 28133
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 1.62 1.66 100 1.871 2.031 0.785 0.399 6.6 2096
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 1.62 44.24 26713 1386 99.93 0.1905 0.1893 0.2627 0.2138 0.2748 RANDOM 29.932
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] -0.35 -0.35 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.138 r_dihedral_angle_3_deg 15.249 r_dihedral_angle_4_deg 12.624 r_dihedral_angle_1_deg 7.873 r_mcangle_it 4.12 r_mcbond_other 2.327 r_mcbond_it 2.311 r_angle_refined_deg 1.63 r_angle_other_deg 1.343 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.138 r_dihedral_angle_3_deg 15.249 r_dihedral_angle_4_deg 12.624 r_dihedral_angle_1_deg 7.873 r_mcangle_it 4.12 r_mcbond_other 2.327 r_mcbond_it 2.311 r_angle_refined_deg 1.63 r_angle_other_deg 1.343 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1190 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing