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SpNOX dehydrogenase domain, mutant F397W in complex with Flavin adenine dinucleotide (FAD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Homology model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Crystals Obtained at the HTX Facility, EMBL Grenoble
17% w/v PEG3350, 0.1M BIS-TRIS Propane pH6.5, 0.2M Sodium bromide.
Automatic harvesting and cryocooling with CrystalDirect
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.622 α = 90 b = 104.622 β = 90 c = 142.688 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 PILATUS 6M Vertical CRL / Horizontal elliptical mirror 2018-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9184 ESRF ID30B
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 1.941 58.944 98.4 0.117 0.119 0.023 0.998 21.2 13.8 57719
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.941 1.974 95.6 1.829 0.372 0.723 2.1 12.9
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 1.941 36.99 57709 2885 97.6 0.1919 0.1902 0.1869 0.2249 0.2203 RANDOM 38.64
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] -0.3933 -0.3933 0.7865
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.82 t_omega_torsion 3.51 t_angle_deg 0.91 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5304 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 185
Software Software Software Name Purpose BUSTER refinement MxCuBE data collection CRANK2 phasing Aimless data scaling autoPROC data processing Coot model building XDS data reduction