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Crystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with M41 and NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CAK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8 293 0.3 M diethylene glycol; 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, Tris-HCl 0.1 M pH 8.0, 20% (v/v) ethylene glycol, 10% (w/v) PEG8000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.683 α = 90 b = 128.683 β = 90 c = 72.106 γ = 120
Symmetry Space Group P 3 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 PILATUS 6M 2022-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.967700 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.5 72.21 99.9 0.172 0.177 0.039 0.999 17.5 20.5 24102
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 100 2.676 2.742 0.592 0.526 21.3
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 8CAK 2.5 72.21 22942 1156 99.87 0.21346 0.21268 0.2163 0.22795 0.2306 RANDOM 51.514
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 0.95 -3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.807 r_dihedral_angle_4_deg 20.149 r_dihedral_angle_3_deg 16.402 r_long_range_B_refined 12.736 r_long_range_B_other 12.734 r_scangle_other 10.633 r_dihedral_angle_1_deg 8.354 r_mcangle_it 8.127 r_mcangle_other 8.126 r_scbond_it 7.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.807 r_dihedral_angle_4_deg 20.149 r_dihedral_angle_3_deg 16.402 r_long_range_B_refined 12.736 r_long_range_B_other 12.734 r_scangle_other 10.633 r_dihedral_angle_1_deg 8.354 r_mcangle_it 8.127 r_mcangle_other 8.126 r_scbond_it 7.193 r_scbond_other 7.189 r_mcbond_it 5.656 r_mcbond_other 5.654 r_angle_refined_deg 1.968 r_angle_other_deg 1.368 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.003 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 2028 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 137
Software Software Software Name Purpose Aimless data scaling REFMAC refinement XDS data reduction PHASES phasing