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30S ribosomal protein S24e from Thermococcus barophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0,1 M MES pH 6,5, 30 %(v/v) PEG 300
Crystal Properties Matthews coefficient Solvent content 2.18 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.306 α = 91.36 b = 35.067 β = 89.95 c = 48.897 γ = 92.18
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2021-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.71 48.88 92 0.936 1.6 1.72 15519
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.83 0.255
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 7ZVM 1.71 48.88 14883 785 89.56 0.18775 0.18578 0.2007 0.22514 0.2347 RANDOM 28.822
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] -13.21 5.07 -0.7 2.01 1.75 11.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.022 r_dihedral_angle_1_deg 6.723 r_rigid_bond_restr 5.912 r_scangle_other 5.439 r_scbond_it 5.162 r_scbond_other 5.162 r_long_range_B_other 5.076 r_long_range_B_refined 5.066 r_dihedral_angle_2_deg 4.561 r_mcangle_it 4.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.022 r_dihedral_angle_1_deg 6.723 r_rigid_bond_restr 5.912 r_scangle_other 5.439 r_scbond_it 5.162 r_scbond_other 5.162 r_long_range_B_other 5.076 r_long_range_B_refined 5.066 r_dihedral_angle_2_deg 4.561 r_mcangle_it 4.453 r_mcangle_other 4.451 r_mcbond_it 4.2 r_mcbond_other 4.197 r_angle_refined_deg 1.485 r_angle_other_deg 0.528 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1300 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing