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Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PRM PDB ENTRY 3PRM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 22-28% PEG 8000, 100 mM Na cacodylate pH 6.5, 100-250 mM Mg acetate, and 2% n-Octyl- -D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 40.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.316 α = 90 b = 105.845 β = 90 c = 113.032 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2010-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.978 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.699 77.26 96.5 0.055 50853
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.699 1.76 74.2 0.186 2.8
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 PDB ENTRY 3PRM 1.699 77.26 50853 2581 96.54 0.174 0.172 0.171 0.212 0.2106 RANDOM 25.511
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] -1.2 -0.43 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.731 r_dihedral_angle_4_deg 17.176 r_dihedral_angle_3_deg 12.553 r_dihedral_angle_1_deg 5.881 r_scangle_it 3.138 r_scbond_it 1.985 r_angle_refined_deg 1.351 r_mcangle_it 1.136 r_mcbond_it 0.625 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.731 r_dihedral_angle_4_deg 17.176 r_dihedral_angle_3_deg 12.553 r_dihedral_angle_1_deg 5.881 r_scangle_it 3.138 r_scbond_it 1.985 r_angle_refined_deg 1.351 r_mcangle_it 1.136 r_mcbond_it 0.625 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3788 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 8
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling