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Structure of Thermus thermophilus ribosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KIQ PDB ENTRIES 3KIQ,3KIR experimental model PDB 3KIR PDB ENTRIES 3KIQ,3KIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.1 0.1 M TRIS-HAC PH 7.2, 0.2 M KSCN, 4.1%-4.3% (W/V) PEG 20K AND 4.1%-4.3% (W/V) PEG 550MME
Crystal Properties Matthews coefficient Solvent content 3.3 62.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.594 α = 90 b = 455.434 β = 90 c = 616.94 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2012-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 3.35 50 99.7 0.15 9.3 5.1 842970 1.6 75.6
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 3.35 3.4 99.8 1.06 1.6 4.7
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 3KIQ,3KIR 3.35 49.79 842969 38866 99.6 0.223 0.223 0.2225 0.261 RANDOM 117.5
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] -4.63 -3.68 8.31
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 28.9 c_improper_angle_d 1.51 c_angle_deg 1.2 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 28.9 c_improper_angle_d 1.51 c_angle_deg 1.2 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20551 Nucleic Acid Atoms 35849 Solvent Atoms Heterogen Atoms 155
Software Software Software Name Purpose CNS model building CNS refinement CNS data reduction CNS data scaling CNS phasing