☰ Navigation Tabs
USP15 D1D2 in catalytically-competent state bound to mitoxantrone stack (isoform 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GHA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 Sodium Hepes 0.1M, pH 7.0, PEG8000 5%.
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.882 α = 90 b = 97.399 β = 90.01 c = 62.995 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M X-ray 2019-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.98 97.4 97 0.039 0.045 0.023 0.999 17.6 3.9 51964
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 1.98 2.03 90.7 0.235 0.272 0.134 0.963 4
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 MOLECULAR REPLACEMENT THROUGHOUT 6gha 1.98 44.89 49498 2444 96.7 0.2057 0.2041 0.2121 0.2379 0.2402 RANDOM 51.027
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] -4.9 0.51 9.84 -4.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.217 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_3_deg 11.994 r_dihedral_angle_1_deg 6.423 r_angle_refined_deg 1.51 r_angle_other_deg 1.34 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.217 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_3_deg 11.994 r_dihedral_angle_1_deg 6.423 r_angle_refined_deg 1.51 r_angle_other_deg 1.34 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5604 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 392
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building