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Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Tris-HCl, pH 8.0, 200 mM Li2SO4, 16% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.98 58.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.447 α = 98.64 b = 73.405 β = 93.8 c = 108.142 γ = 100.44
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2017-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 3 106.42 98.9 0.07 20.4 3.9 41897
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 3.05 0.564
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WXM 3 106.42 39737 2154 98.59 0.20311 0.1991 0.1972 0.27922 0.272 RANDOM 82.131
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] -1.85 3.03 -3.36 2.3 1.71 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_3_deg 17.75 r_dihedral_angle_4_deg 17.103 r_long_range_B_refined 7.35 r_long_range_B_other 7.348 r_dihedral_angle_1_deg 6.444 r_mcangle_it 4.636 r_mcangle_other 4.636 r_scangle_other 4.456 r_mcbond_it 2.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_3_deg 17.75 r_dihedral_angle_4_deg 17.103 r_long_range_B_refined 7.35 r_long_range_B_other 7.348 r_dihedral_angle_1_deg 6.444 r_mcangle_it 4.636 r_mcangle_other 4.636 r_scangle_other 4.456 r_mcbond_it 2.806 r_mcbond_other 2.806 r_scbond_it 2.594 r_scbond_other 2.594 r_angle_refined_deg 1.316 r_angle_other_deg 0.926 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12375 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing