☰ Navigation Tabs
Deubiquitinase DUB16 from Leishmania donovani
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UCH All protein atoms
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Sitting drops composed of equal volumes of protein at 16 mg.ml-1 in 150 mM NaCl, 25 mM Tris-HCl pH 8.0, 1 mM DTT and a crystallisation solution of 1.9 M ammonium sulphate in bis-Tris propane buffer (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.66 53.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.4 α = 90 b = 86.4 β = 90 c = 125.57 γ = 120
Symmetry Space Group P 31 2 1
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 2M 2020-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.69 74.48 100 0.06 0.063 0.019 1 19.4 19.7 60298
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) 1.69 1.72 99.8 3.738 3.956 1.29 0.42 0.5 18.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 74.48 60250 3018 99.98 0.212 0.2106 0.2092 0.2425 0.2419 44.257
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] -0.56 -0.28 -0.56 1.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.372 r_dihedral_angle_3_deg 14 r_dihedral_angle_2_deg 13.421 r_lrange_it 8.807 r_lrange_other 8.732 r_scangle_it 6.994 r_scangle_other 6.993 r_dihedral_angle_1_deg 6.831 r_mcangle_other 5.196 r_mcangle_it 5.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.372 r_dihedral_angle_3_deg 14 r_dihedral_angle_2_deg 13.421 r_lrange_it 8.807 r_lrange_other 8.732 r_scangle_it 6.994 r_scangle_other 6.993 r_dihedral_angle_1_deg 6.831 r_mcangle_other 5.196 r_mcangle_it 5.194 r_scbond_it 4.634 r_scbond_other 4.632 r_mcbond_it 3.887 r_mcbond_other 3.886 r_angle_refined_deg 1.603 r_angle_other_deg 0.561 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.209 r_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.164 r_nbd_other 0.146 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3395 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms
Software Software Software Name Purpose DIALS data collection autoPROC data processing xia2 data reduction MOLREP phasing BUCCANEER model building REFMAC refinement