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Crystal Structure of Coxsackievirus B3 3D polymerase in complex with GPC-N143
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 50mM Tris pH 7.5, 24.5% (w/v) Glycerol, 1,29M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 3.75 67.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.62 α = 90 b = 74.62 β = 90 c = 288.43 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 2.7 72.2 96.8 0.072 0.07 9.2 3.6 21638
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) 2.7 2.85 95.8 0.471 0.4 3.3
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 3DDK 2.7 72.2 21638 1168 97.25 0.20607 0.20415 0.2053 0.24072 0.2358 RANDOM 49.647
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] 0.24 0.24 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.833 r_dihedral_angle_3_deg 19.026 r_dihedral_angle_4_deg 18.87 r_dihedral_angle_1_deg 6.415 r_scangle_it 4.204 r_scbond_it 2.517 r_angle_refined_deg 1.793 r_mcangle_it 1.753 r_mcbond_it 0.9 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.833 r_dihedral_angle_3_deg 19.026 r_dihedral_angle_4_deg 18.87 r_dihedral_angle_1_deg 6.415 r_scangle_it 4.204 r_scbond_it 2.517 r_angle_refined_deg 1.793 r_mcangle_it 1.753 r_mcbond_it 0.9 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3770 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing