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PRRSV-1 PLP2 domain bound to ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ 1ubq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20% PEG 3350, 0.2M Mg(NO3)2
Crystal Properties Matthews coefficient Solvent content 3.38 63.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.686 α = 90 b = 159.492 β = 90 c = 147.325 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 IMAGE PLATE RIGAKU RAXIS IV++ 2017-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.85 45.84 97.1 0.987 7.9 4.7 24728
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 9.01 0.685
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 1ubq 2.85 43.94 23538 1156 96.45 0.21408 0.21247 0.2198 0.24658 0.2605 RANDOM 44.2
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] -2.57 2.14 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.674 r_dihedral_angle_4_deg 16.624 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 5.937 r_long_range_B_refined 4.217 r_long_range_B_other 4.205 r_mcangle_it 1.756 r_mcangle_other 1.756 r_scangle_other 1.417 r_angle_refined_deg 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.674 r_dihedral_angle_4_deg 16.624 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 5.937 r_long_range_B_refined 4.217 r_long_range_B_other 4.205 r_mcangle_it 1.756 r_mcangle_other 1.756 r_scangle_other 1.417 r_angle_refined_deg 1.18 r_mcbond_other 0.973 r_mcbond_it 0.972 r_angle_other_deg 0.954 r_scbond_it 0.772 r_scbond_other 0.772 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5577 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 61
Software Software Software Name Purpose PDB-REDO refinement XDS data reduction XDS data scaling PHASER phasing