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Crystal structure of a putative UBL domain of USP9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% PEG 8000, 0.2 M NaCl, 0.1 M HEPES pH7.5, 5% MPD
Crystal Properties Matthews coefficient Solvent content 1.74 29.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.723 α = 90 b = 125.294 β = 90 c = 29.546 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS3 X 6M 2016-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97914 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 50 99.8 0.058 0.061 0.018 7.5 11.7 14247
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 1.5 1.53 99.9 0.857 0.902 0.278 0.891 10.1
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 (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 1.5 50 13525 713 98.85 0.2276 0.2271 0.2313 0.236 0.2423 RANDOM 31.182
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] 2.06 -0.89 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_dihedral_angle_4_deg 13.907 r_dihedral_angle_3_deg 11.168 r_dihedral_angle_1_deg 5.914 r_angle_refined_deg 1.426 r_angle_other_deg 0.915 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_dihedral_angle_4_deg 13.907 r_dihedral_angle_3_deg 11.168 r_dihedral_angle_1_deg 5.914 r_angle_refined_deg 1.426 r_angle_other_deg 0.915 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 653 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 3
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Arcimboldo phasing Coot model building HKL-3000 data reduction