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Complex with iodine ion for thiocyanate dehydrogenase from Thioalkalivibrio paradoxus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 296 PROTEIN SOLUTION: 10 MG/ML PROTEIN, 25
MM BORATE BUFFER (PH 9.5). PRECIPITANT SOLUTION: 0.025 M AMMONIUM IODIDE, 20.0 % W/V PEG 3350. VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K
Crystal Properties Matthews coefficient Solvent content 2.43 49.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.82 α = 90 b = 159.45 β = 97.77 c = 91 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 100 PIXEL DECTRIS PILATUS3 6M 2016-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.900 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2 30 93.7 0.155 0.996 11.5 6 124180
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 94.5 0.861 0.764 2.35 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 5F30 2 30 118078 6102 93.66 0.15784 0.15573 0.1558 0.19841 0.1985 RANDOM 21.175
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] 0.95 -0.47 -1.02 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.275 r_dihedral_angle_4_deg 18.746 r_dihedral_angle_3_deg 14.593 r_dihedral_angle_1_deg 7.322 r_long_range_B_refined 5.367 r_scbond_it 2.908 r_mcangle_it 2.344 r_angle_refined_deg 2.018 r_mcbond_it 1.652 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.275 r_dihedral_angle_4_deg 18.746 r_dihedral_angle_3_deg 14.593 r_dihedral_angle_1_deg 7.322 r_long_range_B_refined 5.367 r_scbond_it 2.908 r_mcangle_it 2.344 r_angle_refined_deg 2.018 r_mcbond_it 1.652 r_chiral_restr 0.143 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 14572 Nucleic Acid Atoms Solvent Atoms 919 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing