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Structure of CsoS4B from Halothiobacillus neapolitanus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 30% polyethylene glycol 400, 0.2 M Li2SO4 and 0.1 M sodium cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.337 α = 90 b = 68.434 β = 124.42 c = 70.907 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2018-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97918 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 50 98.1 0.187 0.187 10.259 3.8 20226
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 98.5 0.678 0.678 3.41 3.3
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 2rcf 2.15 40.18 19213 1013 97.2 0.17248 0.16969 0.1763 0.2266 0.2308 RANDOM 32.206
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] -1.49 0.36 -0.53 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.354 r_dihedral_angle_4_deg 17.655 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_1_deg 7.609 r_long_range_B_refined 7.141 r_long_range_B_other 7.12 r_scangle_other 5.54 r_scbond_it 3.643 r_scbond_other 3.633 r_mcangle_it 3.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.354 r_dihedral_angle_4_deg 17.655 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_1_deg 7.609 r_long_range_B_refined 7.141 r_long_range_B_other 7.12 r_scangle_other 5.54 r_scbond_it 3.643 r_scbond_other 3.633 r_mcangle_it 3.594 r_mcangle_other 3.593 r_mcbond_it 2.495 r_mcbond_other 2.495 r_angle_refined_deg 1.524 r_angle_other_deg 1.261 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 2899 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing