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Structure of human adenovirus 2 protease with cofactor pVIC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 277.15 Grew over one week at 4 degrees Celsius in 0.1 M sodium citrate pH 6.4, 1.7 M sodium acetate, 1 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.71 66.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.42 α = 90 b = 112.42 β = 90 c = 49.5 γ = 120
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 RIGAKU SATURN 70 2015-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 97.36 97.7 0.059 0.065 16 5.54 20733
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 2.1 2.18 95.7 0.196 6 4.46
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 1AVP 2.1 97.36 19700 1033 98.3 0.17663 0.17554 0.1902 0.19691 0.208 RANDOM 13.214
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] 0.48 0.24 0.48 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.99 r_dihedral_angle_4_deg 14.833 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 7.877 r_long_range_B_refined 6.402 r_long_range_B_other 6.067 r_scangle_other 2.956 r_scbond_it 1.929 r_scbond_other 1.929 r_mcangle_it 1.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.99 r_dihedral_angle_4_deg 14.833 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 7.877 r_long_range_B_refined 6.402 r_long_range_B_other 6.067 r_scangle_other 2.956 r_scbond_it 1.929 r_scbond_other 1.929 r_mcangle_it 1.847 r_mcangle_other 1.846 r_angle_refined_deg 1.588 r_mcbond_it 1.242 r_mcbond_other 1.242 r_angle_other_deg 0.996 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1707 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing d*TREK data scaling d*TREK data reduction