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RNA-dependent RNA polymerase of foot-and-mouth disease virus in complex with a template-primer RNA and ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U09 PDB ENTRY 1U09
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 30% PEG 4000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.656 α = 90 b = 95.656 β = 90 c = 201.458 γ = 120
Symmetry Space Group P 31 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 197 CCD ADSC QUANTUM 4 2004-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93 ESRF ID14-2
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 30 95 0.075 0.054 7.6 30133 28495 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 PDB ENTRY 1U09 2.75 20 2 2 23062 1223 85.49 0.24741 0.24486 0.2757 0.29548 0.3186 RANDOM 52.027
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] 0.35 0.18 0.35 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.805 r_dihedral_angle_3_deg 17.703 r_dihedral_angle_4_deg 16.264 r_dihedral_angle_1_deg 4.968 r_scangle_it 1.37 r_angle_refined_deg 1.15 r_scbond_it 0.808 r_mcangle_it 0.761 r_mcbond_it 0.422 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.805 r_dihedral_angle_3_deg 17.703 r_dihedral_angle_4_deg 16.264 r_dihedral_angle_1_deg 4.968 r_scangle_it 1.37 r_angle_refined_deg 1.15 r_scbond_it 0.808 r_mcangle_it 0.761 r_mcbond_it 0.422 r_nbtor_refined 0.303 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.08 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7428 Nucleic Acid Atoms 638 Solvent Atoms 114 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement ProDC data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing