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Crystal structure of the SRP54-SRP19-7S.S SRP RNA complex of M. jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LNG PDB ENTRY 1LNG
Crystallization Crystal Properties Matthews coefficient Solvent content 2.15 40.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.286 α = 90 b = 129.402 β = 90 c = 163.417 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 CCD MARRESEARCH 2004-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.5 30 99.1 0.13 6.3 5.6 49835 2
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 2.5 2.6 95.2 0.76 1.6 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LNG 2.5 20 48767 2620 99.6 0.247 0.244 0.294 RANDOM 50.42
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] -3.26 -3.41 6.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.895 r_scangle_it 4.257 r_dihedral_angle_1_deg 3.774 r_scbond_it 2.956 r_angle_refined_deg 2.953 r_mcangle_it 1.243 r_mcbond_it 0.687 r_symmetry_vdw_refined 0.367 r_nbd_refined 0.355 r_symmetry_hbond_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.895 r_scangle_it 4.257 r_dihedral_angle_1_deg 3.774 r_scbond_it 2.956 r_angle_refined_deg 2.953 r_mcangle_it 1.243 r_mcbond_it 0.687 r_symmetry_vdw_refined 0.367 r_nbd_refined 0.355 r_symmetry_hbond_refined 0.295 r_xyhbond_nbd_refined 0.291 r_chiral_restr 0.136 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7736 Nucleic Acid Atoms 4126 Solvent Atoms 474 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CNS phasing