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FMDV 3D polymerase crystallized in presence of (F)uridylylated VPg peptide
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 0.2M ammonium acetate, 30% PEG 4K,
0.1M MES pH 6.0, 4 butyrolactone
Crystal Properties Matthews coefficient Solvent content 2.47 50.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.85 α = 90 b = 93.85 β = 90 c = 121.31 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 173 PIXEL DECTRIS PILATUS3 S 6M 2011-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97692 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.3 74.23 99.9 0.092 0.039 12.7 6.6 24747
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 100 0.777 0.319 2.5 6.9
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 2.3 74.23 23429 1257 99.8 0.20011 0.19738 0.2012 0.25203 0.251 RANDOM 45.302
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] -1.01 -1.01 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.54 r_dihedral_angle_3_deg 16.285 r_dihedral_angle_4_deg 16.144 r_dihedral_angle_1_deg 6.208 r_long_range_B_refined 4.29 r_long_range_B_other 4.289 r_mcangle_it 2.056 r_mcangle_other 2.055 r_scangle_other 1.927 r_angle_refined_deg 1.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.54 r_dihedral_angle_3_deg 16.285 r_dihedral_angle_4_deg 16.144 r_dihedral_angle_1_deg 6.208 r_long_range_B_refined 4.29 r_long_range_B_other 4.289 r_mcangle_it 2.056 r_mcangle_other 2.055 r_scangle_other 1.927 r_angle_refined_deg 1.243 r_angle_other_deg 1.188 r_mcbond_it 1.164 r_mcbond_other 1.164 r_scbond_it 1.103 r_scbond_other 1.103 r_chiral_restr 0.053 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 3743 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing