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Crystal structure of a hybrid ribosomal protein L30e with surface residues from T. celer, and core residues from yeast
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H7M PDB ENTRY 1H7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 2UL 10MG/ML PROTEIN AND 2UL 22.5% PEG3350, 0.1M TRIS PH 8.5, CRYOPROTECTED IN 20% PEG 400
Crystal Properties Matthews coefficient Solvent content 1.58 21.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.187 α = 90 b = 52.531 β = 90 c = 52.692 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 CCD BRUKER M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6B PAL/PLS 6B
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 1.7 20 98.6 0.06 63 5.6 9277 63
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 1.7 1.76 94.9 0.09 34 4.6
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 PDB ENTRY 1H7M 1.7 37.19 8796 445 98.5 0.176 0.173 0.187 0.24 0.2435 RANDOM 8.22
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] 0.22 -0.14 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.284 r_dihedral_angle_3_deg 12.91 r_dihedral_angle_4_deg 10.663 r_dihedral_angle_1_deg 5.518 r_scangle_it 3.465 r_scbond_it 2.31 r_angle_refined_deg 1.305 r_mcbond_it 1.21 r_mcangle_it 1.208 r_angle_other_deg 0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.284 r_dihedral_angle_3_deg 12.91 r_dihedral_angle_4_deg 10.663 r_dihedral_angle_1_deg 5.518 r_scangle_it 3.465 r_scbond_it 2.31 r_angle_refined_deg 1.305 r_mcbond_it 1.21 r_mcangle_it 1.208 r_angle_other_deg 0.776 r_symmetry_vdw_other 0.255 r_nbd_refined 0.208 r_nbtor_refined 0.175 r_nbd_other 0.163 r_xyhbond_nbd_refined 0.127 r_symmetry_vdw_refined 0.12 r_symmetry_hbond_refined 0.097 r_nbtor_other 0.081 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 780 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction DENZO data reduction HKL-2000 data scaling SCALEPACK data scaling CNS phasing