☰ Navigation Tabs
PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1545313172 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 61.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.52 α = 90 b = 54.52 β = 90 c = 75.36 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 1.48 37.68 100 0.038 0.042 0.016 1 20.9 6.6 36721
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 1.48 1.52 99.9 1.445 1.567 0.602 0.507 6.7 2706
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2NVH 1.48 34.34 34832 1852 99.96 0.1969 0.1955 0.2225 0.2949 RANDOM 29.509
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 33.278 r_dihedral_angle_3_deg 13.849 r_dihedral_angle_4_deg 11.108 r_dihedral_angle_1_deg 8.418 r_mcangle_it 4.41 r_mcbond_other 2.921 r_mcbond_it 2.854 r_angle_refined_deg 1.922 r_angle_other_deg 1.387 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.278 r_dihedral_angle_3_deg 13.849 r_dihedral_angle_4_deg 11.108 r_dihedral_angle_1_deg 8.418 r_mcangle_it 4.41 r_mcbond_other 2.921 r_mcbond_it 2.854 r_angle_refined_deg 1.922 r_angle_other_deg 1.387 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 124 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing