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Tetragonal structure of mutant V173I of 3D polymerase from Foot-and-Mouth Disease Virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U09
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 36% PEG4000
0.2M Ammonium acetate
0.1M MES pH6.0
4% gamma-butyrolactone
Crystal Properties Matthews coefficient Solvent content 2.42 49.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.537 α = 90 b = 92.537 β = 90 c = 120.441 γ = 90
Symmetry Space Group P 41 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 DECTRIS PILATUS3 6M 2013-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.59 46.27 99.2 0.086 12.2 4.3 16540
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.73 96.3 0.765
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 1U09 2.6 46.27 15685 834 98.89 0.23029 0.22826 0.2299 0.27083 0.2699 RANDOM 63.117
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] 0.07 0.07 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.219 r_dihedral_angle_3_deg 13.327 r_dihedral_angle_4_deg 10.209 r_dihedral_angle_1_deg 4.88 r_long_range_B_refined 2.094 r_long_range_B_other 2.093 r_angle_other_deg 1.13 r_angle_refined_deg 1.035 r_mcangle_it 0.713 r_mcangle_other 0.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.219 r_dihedral_angle_3_deg 13.327 r_dihedral_angle_4_deg 10.209 r_dihedral_angle_1_deg 4.88 r_long_range_B_refined 2.094 r_long_range_B_other 2.093 r_angle_other_deg 1.13 r_angle_refined_deg 1.035 r_mcangle_it 0.713 r_mcangle_other 0.713 r_mcbond_it 0.376 r_mcbond_other 0.376 r_scangle_other 0.348 r_scbond_it 0.162 r_scbond_other 0.157 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 3742 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing