☰ Navigation Tabs
Structure of SpNOX: a Bacterial NADPH oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model ITasser experimental model PDB 8QQ5 Seperate search of TM domain, manually edited from 5o0t, and DH domain solved by Xray structure.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein: 4.04 mg/ml in 50 mM Tris pH 7, 300 mM NaCl, 0.025 mM MNG3, 0.01 mM FAD.
Crystallization condition: 30.5% PEG 300, 0.15 M Li2SO4, 0.15 M NaCl and 0.1 M MES pH6.
Drop: 6 uL of protein + 6 uL of well.
Crystal Properties Matthews coefficient Solvent content 5.11 75.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.967 α = 90 b = 145.967 β = 90 c = 153.619 γ = 120
Symmetry Space Group P 64 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 PIXEL DECTRIS PILATUS3 2M 2018-05-11 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.62 47.82 90.9 0.072 0.074 0.017 19.6 20 5508
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.62 3.95 85.4 2 0.465 1.5 20
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 model from PROMALS3D and I-TASSER 3.62 47.82 5262 245 47.85 0.2642 0.26152 0.3346 0.32003 0.334 RANDOM 201.602
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] 1.73 0.86 1.73 -5.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.378 r_mcangle_it 31.664 r_scbond_it 23.462 r_mcbond_it 19.415 r_dihedral_angle_4_deg 19.245 r_dihedral_angle_3_deg 17.803 r_dihedral_angle_1_deg 8.416 r_angle_refined_deg 1.727 r_chiral_restr 0.135 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.378 r_mcangle_it 31.664 r_scbond_it 23.462 r_mcbond_it 19.415 r_dihedral_angle_4_deg 19.245 r_dihedral_angle_3_deg 17.803 r_dihedral_angle_1_deg 8.416 r_angle_refined_deg 1.727 r_chiral_restr 0.135 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 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_refined 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 3404 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling STARANISO data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction