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Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10-25% PEG 2K or 3K, 100 mM Na Acetate or Na Citrate, pH 4.5 - 4.9
Protein conc 10 mg/ml
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.389 α = 90 b = 106.389 β = 90 c = 67.486 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 S 6M 2017-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 67.48 100 0.071 0.074 1 18.2 20.7 36515 22.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 100 2.595 2.725 0.644 1.3 21.3
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 5A8B 1.5 67.48 34209 1886 98.91 0.17476 0.17304 0.1782 0.20501 0.1689 RANDOM 26.378
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] -0.39 -0.19 -0.39 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.594 r_sphericity_free 27.908 r_dihedral_angle_3_deg 14.797 r_dihedral_angle_4_deg 14.495 r_sphericity_bonded 8.616 r_dihedral_angle_1_deg 6.054 r_long_range_B_refined 3.884 r_long_range_B_other 3.883 r_rigid_bond_restr 2.754 r_scangle_other 2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.594 r_sphericity_free 27.908 r_dihedral_angle_3_deg 14.797 r_dihedral_angle_4_deg 14.495 r_sphericity_bonded 8.616 r_dihedral_angle_1_deg 6.054 r_long_range_B_refined 3.884 r_long_range_B_other 3.883 r_rigid_bond_restr 2.754 r_scangle_other 2.7 r_scbond_other 2.438 r_scbond_it 2.437 r_mcangle_other 2.319 r_mcangle_it 2.317 r_angle_refined_deg 2.006 r_mcbond_it 1.828 r_mcbond_other 1.814 r_angle_other_deg 1.044 r_chiral_restr 0.141 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1057 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling MOLREP phasing