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Crystal structure of 7S.S SRP RNA of M. jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LNG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 PEG 400, Tris buffer, sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.64 66.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.11 α = 90 b = 62.11 β = 90 c = 247.52 γ = 90
Symmetry Space Group P 43 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.081 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 20 98.9 15814 15645 78570
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.7 98.6 1632
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 (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 1LNG 2.6 20 15640 14857 783 98.9 0.2552 0.2531 0.2651 0.29616 0.3052 RANDOM 37.874
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] 2.44 2.44 -4.88
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 3.226 r_scangle_it 3.007 r_scbond_it 2.05 r_angle_other_deg 2.024 r_nbd_other 0.36 r_nbd_refined 0.32 r_symmetry_hbond_refined 0.274 r_xyhbond_nbd_refined 0.246 r_symmetry_vdw_refined 0.243 r_symmetry_vdw_other 0.159
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 3.226 r_scangle_it 3.007 r_scbond_it 2.05 r_angle_other_deg 2.024 r_nbd_other 0.36 r_nbd_refined 0.32 r_symmetry_hbond_refined 0.274 r_xyhbond_nbd_refined 0.246 r_symmetry_vdw_refined 0.243 r_symmetry_vdw_other 0.159 r_xyhbond_nbd_other 0.128 r_chiral_restr 0.114 r_nbtor_other 0.026 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2169 Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling CNS phasing