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structure of the rna binding domain of n protein from SARS coronavirus in cubic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OFZ pdb entry 2ofz
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 277 40% MPD and 0.1 M Tris pH 8.0, typically crystals appear within 2 weeks, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.6 65.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.001 α = 90 b = 110.001 β = 90 c = 110.001 γ = 90
Symmetry Space Group I 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD mirrors 2005-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9797 SSRL BL11-1
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 1.85 38.9 99.78 0.075 0.068 29.33 4.1 18018 17989 29.19
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) 1.85 1.89 100 0.47 0.44 1.91 1.9 1330
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2ofz 1.85 38.9 17989 17989 976 99.78 0.1961 0.20133 0.19904 0.24711 0.2627 RANDOM 29.19
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.272 r_dihedral_angle_4_deg 22.427 r_dihedral_angle_3_deg 16.017 r_dihedral_angle_1_deg 6.377 r_scangle_it 3.685 r_scbond_it 2.292 r_mcangle_it 1.658 r_angle_refined_deg 1.431 r_mcbond_it 1.012 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.272 r_dihedral_angle_4_deg 22.427 r_dihedral_angle_3_deg 16.017 r_dihedral_angle_1_deg 6.377 r_scangle_it 3.685 r_scbond_it 2.292 r_mcangle_it 1.658 r_angle_refined_deg 1.431 r_mcbond_it 1.012 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.262 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_refined 0.18 r_chiral_restr 0.117 r_metal_ion_refined 0.053 r_symmetry_metal_ion_refined 0.02 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 889 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing