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RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NKW PDB ENTRY 1NKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 290 ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 4 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.7 α = 90 b = 405 β = 90 c = 693 γ = 90
Symmetry Space Group I 2 2 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 CCD MARRESEARCH 2004-04-14 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 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 3.3 30 95.2 0.104 9.8 343272 343272 28.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.3 3.36 86.8 0.398 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MR THROUGHOUT PDB ENTRY 1NKW 3.33 8.13 1 343272 238082 11832 74.5 0.291 0.275 0.275 0.364 0.338 0.3913 RANDOM 50
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] -20.39 48.11 -27.72
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.2 c_improper_angle_d 1.62 c_angle_deg 1.3 c_bond_d 0.008 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 18.2 c_improper_angle_d 1.62 c_angle_deg 1.3 c_bond_d 0.008 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 2609 Nucleic Acid Atoms 61875 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing