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PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z57475877 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 3.22 61.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.457 α = 90 b = 54.457 β = 90 c = 75.473 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 1.35 54.46 100 0.036 0.039 0.015 0.999 19.3 6.6 47897
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 1.35 1.43 99.9 1.925 2.086 0.798 0.396 6.6 6970
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 1.35 54.46 45393 2359 99.73 0.2028 0.2015 0.2381 0.2279 0.2527 RANDOM 29.145
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] -0.28 -0.28 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.244 r_dihedral_angle_3_deg 14.094 r_dihedral_angle_4_deg 10.836 r_dihedral_angle_1_deg 8.415 r_mcangle_it 4.166 r_mcbond_other 2.376 r_mcbond_it 2.358 r_angle_refined_deg 1.783 r_angle_other_deg 1.392 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.244 r_dihedral_angle_3_deg 14.094 r_dihedral_angle_4_deg 10.836 r_dihedral_angle_1_deg 8.415 r_mcangle_it 4.166 r_mcbond_other 2.376 r_mcbond_it 2.358 r_angle_refined_deg 1.783 r_angle_other_deg 1.392 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 115 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing