☰ Navigation Tabs
PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z2377835233 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 3.24 62.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.73 α = 90 b = 54.73 β = 90 c = 75.25 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 1.41 54.73 100 0.051 0.055 0.022 0.999 16 6.6 42703
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 1.41 1.45 100 1.554 1.697 0.676 0.462 6.2 3133
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 1.41 54.73 40559 2107 99.95 0.192 0.1912 0.2574 0.2075 0.265 RANDOM 26.407
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] -0.32 -0.32 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.565 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_4_deg 8.444 r_dihedral_angle_1_deg 8.22 r_mcangle_it 3.445 r_mcbond_other 1.995 r_mcbond_it 1.988 r_angle_refined_deg 1.707 r_angle_other_deg 1.389 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.565 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_4_deg 8.444 r_dihedral_angle_1_deg 8.22 r_mcangle_it 3.445 r_mcbond_other 1.995 r_mcbond_it 1.988 r_angle_refined_deg 1.707 r_angle_other_deg 1.389 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1190 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing