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Structure of WT SpNox DH domain: a bacterial NADPH oxidase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QQ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein: 15 mg/ml in 100 mM bis-TRIS propane pH 6.5, 300 mM NaCl, 5% glycerol, 0.01 mM FAD.
Crystallization condition: 35% PEG MME 500 and 0.1 M sodium citrate pH5.
Drop: 100 nL of protein +100 nL of well.
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.88 α = 90 b = 104.88 β = 90 c = 139.29 γ = 90
Symmetry Space Group P 41 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 PILATUS3 2M 2018-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 46.9 100 0.999 18.99 25.96 26155
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.639
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 46.9 26155 1377 99.96 0.2014 0.1969 0.2012 0.2896 0.2926 RANDOM 70.243
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] -1.07 -1.07 2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.568 r_dihedral_angle_4_deg 19.276 r_dihedral_angle_3_deg 18.66 r_dihedral_angle_1_deg 7.72 r_angle_refined_deg 1.456 r_chiral_restr 0.107 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5343 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 108
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction