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X-ray structure of NdhS from T. elongatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100mM Sodium acetate trihydrate (pH 4.6), 100mM CdCl2, 38 % (v/v) polyethylene glycol (PEG) 400
Crystal Properties Matthews coefficient Solvent content 3.4 64.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.85 α = 90 b = 58.85 β = 90 c = 225.15 γ = 120
Symmetry Space Group P 65 2 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 CCD RAYONIX MX300HE 2017-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 49.71 100 0.058 1 29 11.6 19195
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 0.399 0.985 8.25 11.6
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 3C4S 1.9 49.71 18235 960 99.95 0.21957 0.21858 0.2266 0.23783 0.2465 RANDOM 28.596
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] 8.77 8.77 -17.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.192 r_dihedral_angle_3_deg 13.19 r_long_range_B_refined 9.987 r_long_range_B_other 9.984 r_dihedral_angle_1_deg 7.381 r_scangle_other 6.929 r_dihedral_angle_4_deg 5.359 r_scbond_it 4.93 r_scbond_other 4.925 r_mcangle_other 4.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.192 r_dihedral_angle_3_deg 13.19 r_long_range_B_refined 9.987 r_long_range_B_other 9.984 r_dihedral_angle_1_deg 7.381 r_scangle_other 6.929 r_dihedral_angle_4_deg 5.359 r_scbond_it 4.93 r_scbond_other 4.925 r_mcangle_other 4.428 r_mcangle_it 4.415 r_mcbond_it 3.206 r_mcbond_other 3.053 r_angle_refined_deg 2.109 r_angle_other_deg 1.078 r_chiral_restr 0.168 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 948 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing