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Crystal structure of flavin reductase (StnC) complexed with FAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1% w/v Tryptone, 0.001M Sodium azide, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.15 42.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.921 α = 90 b = 52.86 β = 90 c = 174.854 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2022-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 1.82 50 97 0.138 0.144 0.041 0.987 4.3 11.6 37829
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 1.82 1.85 93.7 1.039 1.086 0.312 0.75 11.4
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 1.82 45.28 35954 1803 96.85 0.18862 0.18778 0.1959 0.20493 0.2139 RANDOM 21.292
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] -0.03 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.224 r_dihedral_angle_4_deg 17.514 r_dihedral_angle_3_deg 15.134 r_long_range_B_other 8.7 r_long_range_B_refined 8.668 r_scangle_other 5.42 r_dihedral_angle_1_deg 5.117 r_scbond_it 3.389 r_scbond_other 3.384 r_mcangle_other 2.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.224 r_dihedral_angle_4_deg 17.514 r_dihedral_angle_3_deg 15.134 r_long_range_B_other 8.7 r_long_range_B_refined 8.668 r_scangle_other 5.42 r_dihedral_angle_1_deg 5.117 r_scbond_it 3.389 r_scbond_other 3.384 r_mcangle_other 2.414 r_mcangle_it 2.412 r_mcbond_it 1.69 r_mcbond_other 1.666 r_angle_other_deg 1.54 r_angle_refined_deg 1.411 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3357 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction PHASER phasing HKL-3000 data reduction