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Crystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 50 mM Tris pH 7.5, 24.5% (w/v) glycerol, 1.29 M ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 3.78 67.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.74 α = 90 b = 74.74 β = 90 c = 289.05 γ = 90
Symmetry Space Group P 43 21 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 PIXEL PSI PILATUS 6M 2011-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.977 ESRF ID29
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 2.9 72.4 99.8 0.081 0.08 7.6 3.6 18099
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.05 99.5 0.415 0.357 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DDK 2.9 72.36 18099 979 99.66 0.20025 0.19761 0.25049 0.2089 RANDOM 55.837
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] 3.51 3.51 -7.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.027 r_dihedral_angle_3_deg 18.418 r_dihedral_angle_4_deg 17.838 r_long_range_B_refined 9.819 r_long_range_B_other 9.819 r_scangle_other 7.4 r_dihedral_angle_1_deg 6.648 r_mcangle_it 5.802 r_mcangle_other 5.802 r_scbond_it 4.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.027 r_dihedral_angle_3_deg 18.418 r_dihedral_angle_4_deg 17.838 r_long_range_B_refined 9.819 r_long_range_B_other 9.819 r_scangle_other 7.4 r_dihedral_angle_1_deg 6.648 r_mcangle_it 5.802 r_mcangle_other 5.802 r_scbond_it 4.659 r_scbond_other 4.652 r_mcbond_it 3.783 r_mcbond_other 3.769 r_angle_refined_deg 1.712 r_angle_other_deg 1.072 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3727 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing