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CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5COL 5COL, 5D6G experimental model PDB 5D6G 5COL, 5D6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 50 mM Tris-HCl, pH 7.5, 0.15 M KCl, 20 mM MgCl2, 15% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.44 49.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.396 α = 90 b = 88.451 β = 102.19 c = 95.231 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD Bruker Platinum 135 2012-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.9 20 97.4 0.14 7.01 4.35 25542 25542
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 2.9 3 96.9 0.5 2.09 4.4
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5COL, 5D6G 2.9 20 24191 1293 97.2 0.26607 0.26443 0.29679 0.2569 RANDOM 43.6
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] 1.9 -1.58 -0.14 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.881 r_dihedral_angle_3_deg 19.581 r_dihedral_angle_4_deg 17.703 r_long_range_B_refined 9.666 r_long_range_B_other 9.656 r_dihedral_angle_1_deg 7.709 r_mcangle_it 6.334 r_mcangle_other 6.333 r_mcbond_it 3.668 r_mcbond_other 3.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.881 r_dihedral_angle_3_deg 19.581 r_dihedral_angle_4_deg 17.703 r_long_range_B_refined 9.666 r_long_range_B_other 9.656 r_dihedral_angle_1_deg 7.709 r_mcangle_it 6.334 r_mcangle_other 6.333 r_mcbond_it 3.668 r_mcbond_other 3.667 r_scangle_other 3.457 r_angle_other_deg 3.374 r_scbond_it 1.994 r_scbond_other 1.994 r_angle_refined_deg 1.672 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_other_d 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 5208 Nucleic Acid Atoms 3176 Solvent Atoms 14 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing