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The structure of holo- structure of DHAD complex with [2Fe-2S] cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 0.1 M sodium acetate pH 5.0,
1.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.48 50.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.467 α = 90 b = 135.467 β = 90 c = 65.978 γ = 90
Symmetry Space Group P 42 21 2
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 PILATUS 300K 2017-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97774 SSRF BL19U1
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 2.11 50 100 0.189 2 25.1 36139
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 2.11 2.15 1.24
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 5J83 2.11 30 33076 1709 96.86 0.17479 0.17272 0.1857 0.21519 0.225 RANDOM 26.395
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.639 r_sphericity_free 28.22 r_dihedral_angle_4_deg 14.213 r_dihedral_angle_3_deg 11.811 r_dihedral_angle_1_deg 5.805 r_sphericity_bonded 4.776 r_long_range_B_refined 2.098 r_long_range_B_other 2.014 r_mcangle_it 1.618 r_mcangle_other 1.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.639 r_sphericity_free 28.22 r_dihedral_angle_4_deg 14.213 r_dihedral_angle_3_deg 11.811 r_dihedral_angle_1_deg 5.805 r_sphericity_bonded 4.776 r_long_range_B_refined 2.098 r_long_range_B_other 2.014 r_mcangle_it 1.618 r_mcangle_other 1.618 r_scangle_other 1.542 r_mcbond_it 1.234 r_mcbond_other 1.231 r_scbond_it 1.221 r_scbond_other 1.22 r_angle_refined_deg 1.191 r_rigid_bond_restr 1.027 r_angle_other_deg 0.9 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4218 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing