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Structure of ribosome-apramycin complexes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J5E PDB ENTRY 1J5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 MPD, NH4CL, KCL, CACL2, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP AT 277K
Crystal Properties Matthews coefficient Solvent content 4.83 74.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 402.18 α = 90 b = 402.18 β = 90 c = 175 γ = 90
Symmetry Space Group P 41 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 2009-04-25 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 3.5 40 99.7 0.1 16 6.9 178694 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 3.5 3.6 99.5 1.1 2 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1J5E 3.5 40 2 178694 8631 99.8 0.1934 0.1934 0.1976 0.2351 SAME AS 1J5E MODEL
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] -11.282 -11.282 22.563
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.203 c_bond_d 0.0068 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
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.203 c_bond_d 0.0068 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 c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d 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 19220 Nucleic Acid Atoms 32888 Solvent Atoms 1 Heterogen Atoms 405
Software Software Software Name Purpose CNS refinement XDS data reduction XSCALE data scaling