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Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Mn2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG 8000, sodium HEPES, manganese chloride glycerol, hexanediol, 3'-deoxy-ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.92 57.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.694 α = 90 b = 119.845 β = 90 c = 159.498 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2001-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 40 99.9 0.097 0.097 17.4 5.8 37963 37963 -3 -3 69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 100 0.722 0.722 2.4 5.5 3733
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.7 31.16 38016 34165 3795 100 0.241 0.24081 0.23789 0.2284 0.26747 0.2604 RANDOM 28.407
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] 1.5 -2.07 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.422 r_scangle_it 4.119 r_dihedral_angle_1_deg 3.161 r_scbond_it 2.623 r_mcangle_it 1.905 r_angle_refined_deg 1.426 r_mcbond_it 1.116 r_nbd_refined 0.166 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.422 r_scangle_it 4.119 r_dihedral_angle_1_deg 3.161 r_scbond_it 2.623 r_mcangle_it 1.905 r_angle_refined_deg 1.426 r_mcbond_it 1.116 r_nbd_refined 0.166 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.144 r_symmetry_vdw_refined 0.128 r_chiral_restr 0.099 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7776 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing