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Crystal structure of human adenovirus 2 protease a substrate based nitrile inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NLN PDB entry 1NLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 1mM peptide-nitrile inhibitor was added to the protein and incubated for 30 minutes. 0.8M lithium sulphate, 0.1 M sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.86 33.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.312 α = 90 b = 44.437 β = 90 c = 98.921 γ = 90
Symmetry Space Group P 21 21 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 PSI PILATUS 6M 2011-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.94 44.4 99.9 0.054 0.059 19.48 6.4 14072 -3 34.286
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.99 99.7 0.407 0.442 4.57
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 1NLN 1.94 40.53 14072 704 99.95 0.2096 0.2069 0.2091 0.2603 0.2586 RANDOM 31.634
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] -2.49 5.01 -2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.728 r_dihedral_angle_3_deg 17.297 r_dihedral_angle_4_deg 13.089 r_dihedral_angle_1_deg 7.102 r_scangle_it 4.829 r_scbond_it 3.272 r_angle_refined_deg 2.049 r_mcangle_it 1.903 r_mcbond_it 1.113 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.728 r_dihedral_angle_3_deg 17.297 r_dihedral_angle_4_deg 13.089 r_dihedral_angle_1_deg 7.102 r_scangle_it 4.829 r_scbond_it 3.272 r_angle_refined_deg 2.049 r_mcangle_it 1.903 r_mcbond_it 1.113 r_chiral_restr 0.138 r_bond_refined_d 0.024 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1685 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 49
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling