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Trigonal 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 1WNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 36% PEG 4000,
0.2M ammonium acetate
0.1M MES(2-(N-morpholino) ethanesulfonic acid) pH 6.0
4% gamma-butyrolactone.
Crystal Properties Matthews coefficient Solvent content 2.37 48.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.506 α = 90 b = 93.506 β = 90 c = 99.626 γ = 120
Symmetry Space Group P 32 2 1
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 0.987 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 2.4 46.75 96.3 0.043 22 6 20009
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 2.4 2.53 96.3 0.431 2.4 3.6
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 1WNR 2.4 46.75 18995 991 99.27 0.25298 0.25156 0.2462 0.28149 0.2765 RANDOM 73.103
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] 0.08 0.04 0.08 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.367 r_dihedral_angle_4_deg 16.996 r_dihedral_angle_3_deg 16.017 r_dihedral_angle_1_deg 6.124 r_long_range_B_refined 1.564 r_long_range_B_other 1.564 r_angle_refined_deg 1.159 r_angle_other_deg 0.969 r_mcangle_it 0.237 r_mcangle_other 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.367 r_dihedral_angle_4_deg 16.996 r_dihedral_angle_3_deg 16.017 r_dihedral_angle_1_deg 6.124 r_long_range_B_refined 1.564 r_long_range_B_other 1.564 r_angle_refined_deg 1.159 r_angle_other_deg 0.969 r_mcangle_it 0.237 r_mcangle_other 0.237 r_mcbond_it 0.124 r_mcbond_other 0.124 r_scangle_other 0.104 r_chiral_restr 0.066 r_scbond_other 0.046 r_scbond_it 0.045 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3743 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing