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Crystal Structure of the SRP19-7S.S SRP RNA Complex of M. jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D4R PDB entries 1D4R and 1DUL experimental model PDB 1DUL PDB entries 1D4R and 1DUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 273 PEG 3350, HEPES, MgAc, CaCl, DMSO, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.521 α = 90 b = 61.405 β = 90 c = 155.978 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 100 IMAGE PLATE MARRESEARCH 2001-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.12 MAX II I711
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 2.3 20 98.1 0.099 18606 18606
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) 2.3 2.38 91 0.332
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 1D4R and 1DUL 2.3 20 18606 17651 955 98.63 0.22697 0.22697 0.22444 0.27333 RANDOM 38.347
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] -2.02 2.18 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.294 r_dihedral_angle_1_deg 3.917 r_angle_refined_deg 2.704 r_scangle_it 2.539 r_scbond_it 1.684 r_mcangle_it 1.598 r_mcbond_it 0.826 r_symmetry_hbond_refined 0.316 r_nbd_refined 0.273 r_xyhbond_nbd_refined 0.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.294 r_dihedral_angle_1_deg 3.917 r_angle_refined_deg 2.704 r_scangle_it 2.539 r_scbond_it 1.684 r_mcangle_it 1.598 r_mcbond_it 0.826 r_symmetry_hbond_refined 0.316 r_nbd_refined 0.273 r_xyhbond_nbd_refined 0.257 r_symmetry_vdw_refined 0.245 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 727 Nucleic Acid Atoms 2080 Solvent Atoms 200 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CNS refinement DENZO data reduction CCP4 data scaling CNS phasing