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Mutant M16A of RNA dependent RNA polymerase 3D 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 30% PEG 4000, 0.2M magnesium acetate, 0.1M MES[2-(N-morpholino) ethanesulfonic acid] pH 6.0 and 4% a-butyrolactone.
Crystal Properties Matthews coefficient Solvent content 2.43 49.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.12 α = 90 b = 93.12 β = 90 c = 121.05 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 PILATUS 6M 2013-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97166 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 2.35 50 98.1 0.084 0.035 11.4 8 22406
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 2.35 2.48 0.426 2890
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 1U09 2.35 46.6 21246 1110 97.91 0.22171 0.21955 0.26324 0.2714 RANDOM 56.695
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] -1.1 -1.1 2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.65 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_4_deg 12.568 r_dihedral_angle_1_deg 6.207 r_long_range_B_refined 2.851 r_long_range_B_other 2.851 r_mcangle_other 1.16 r_mcangle_it 1.159 r_angle_refined_deg 0.884 r_scangle_other 0.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.65 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_4_deg 12.568 r_dihedral_angle_1_deg 6.207 r_long_range_B_refined 2.851 r_long_range_B_other 2.851 r_mcangle_other 1.16 r_mcangle_it 1.159 r_angle_refined_deg 0.884 r_scangle_other 0.796 r_angle_other_deg 0.737 r_mcbond_it 0.634 r_mcbond_other 0.625 r_scbond_it 0.423 r_scbond_other 0.423 r_chiral_restr 0.041 r_bond_refined_d 0.004 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 3767 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing