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Crystal structure of West Nile Virus NS2B-NS3 protease in complex with a capped dipeptide boronate inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YOL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.2 M magnesium formate, 20% polyethylene (PEG) 3350, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.42 α = 90 b = 96.965 β = 90 c = 187.856 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 Pilatus 6M fast 2015-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.9919 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 46.94 98.6 0.045 0.999 15.6 3.3 105999
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 1.5 1.58 99.3 0.557 2.5 3.4
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 2YOL 1.5 46.94 100708 5227 98.22 0.16052 0.15921 0.1589 0.18577 0.186 RANDOM 21.043
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] 0.05 0.79 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.241 r_dihedral_angle_4_deg 15.439 r_dihedral_angle_3_deg 12.425 r_long_range_B_refined 8.987 r_long_range_B_other 8.986 r_dihedral_angle_1_deg 7.299 r_scangle_other 6.26 r_scbond_it 4.179 r_scbond_other 4.178 r_mcangle_it 4.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.241 r_dihedral_angle_4_deg 15.439 r_dihedral_angle_3_deg 12.425 r_long_range_B_refined 8.987 r_long_range_B_other 8.986 r_dihedral_angle_1_deg 7.299 r_scangle_other 6.26 r_scbond_it 4.179 r_scbond_other 4.178 r_mcangle_it 4.063 r_mcangle_other 4.063 r_mcbond_it 2.72 r_mcbond_other 2.704 r_angle_refined_deg 2.343 r_angle_other_deg 2.264 r_chiral_restr 0.145 r_bond_refined_d 0.025 r_bond_other_d 0.015 r_gen_planes_refined 0.015 r_gen_planes_other 0.011 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 4672 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement MOLREP phasing