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Crystal structure of RNA silencing suppressor p21 from Beet Yellows Virus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2M K/Na Tartrate, 100mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.55 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.633 α = 90 b = 199.633 β = 90 c = 56.122 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 3.3 20 98.82 0.11 21.6 11.3 19491 19263 -3
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 3.3 3.42 95.8 0.66 3 1912
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 MIR THROUGHOUT 3.3 20 18442 18224 943 98.82 0.21168 0.21168 0.21004 0.2115 0.24443 0.2389 RANDOM 132.327
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] -2.79 -1.4 -2.79 4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.517 r_dihedral_angle_3_deg 22.368 r_dihedral_angle_4_deg 20.655 r_dihedral_angle_1_deg 6.244 r_scangle_it 2.501 r_angle_refined_deg 1.812 r_scbond_it 1.439 r_mcangle_it 0.764 r_mcbond_it 0.428 r_symmetry_vdw_refined 0.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.517 r_dihedral_angle_3_deg 22.368 r_dihedral_angle_4_deg 20.655 r_dihedral_angle_1_deg 6.244 r_scangle_it 2.501 r_angle_refined_deg 1.812 r_scbond_it 1.439 r_mcangle_it 0.764 r_mcbond_it 0.428 r_symmetry_vdw_refined 0.374 r_nbtor_refined 0.33 r_nbd_refined 0.272 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.123 r_symmetry_hbond_refined 0.071 r_bond_refined_d 0.019 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_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5388 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing