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Crystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with CA24
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model 5O0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 293 MES 0.1 mM pH 6.5, 0.1 M carboxylic acids, 20% v/v ethylene glycol, 10% w/v PEG8000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.428 α = 90 b = 127.428 β = 90 c = 71.992 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 PILATUS3 2M 2021-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-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 2.3 47.76 99.7 0.203 0.231 0.106 0.964 4.2 4.2 30148
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 2.3 2.38 99.7 1.176 1.342 0.627 0.448 4.2
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 2.3 47.76 28597 1530 99.55 0.217 0.2164 0.2219 0.2264 0.23 RANDOM 56.8627
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] 1.18 0.59 1.18 -3.84
RMS Deviations Key Refinement Restraint Deviation TORSION ANGLES. PERIOD 2 (DEGREES) 34.59 TORSION ANGLES. PERIOD 4 (DEGREES) 19.443 TORSION ANGLES. PERIOD 3 (DEGREES) 16.73 TORSION ANGLES. PERIOD 1 (DEGREES) 8.046 r_angle_refined_deg 2.074 r_angle_other_deg 1.398 r_chiral_restr 0.207 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation TORSION ANGLES. PERIOD 2 (DEGREES) 34.59 TORSION ANGLES. PERIOD 4 (DEGREES) 19.443 TORSION ANGLES. PERIOD 3 (DEGREES) 16.73 TORSION ANGLES. PERIOD 1 (DEGREES) 8.046 r_angle_refined_deg 2.074 r_angle_other_deg 1.398 r_chiral_restr 0.207 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2012 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 116
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing