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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 1.5-3 M Na malonate,
0.1 M Tris.acetate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.18 α = 90 b = 91.51 β = 131.34 c = 99.84 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M 2018-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97625 Diamond I04-1
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 1.66 71.05 98 0.083 0.089 0.997 12 6.1 117045
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 1.66 1.7 99.3 1.029 1.201 0.543 0.9 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5A8B 1.66 71.05 111245 5747 97.9 0.20389 0.20303 0.221 0.2193 RANDOM 36.452
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] -0.34 -0.03 1.49 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.814 r_dihedral_angle_3_deg 15.257 r_dihedral_angle_4_deg 13.434 r_long_range_B_refined 6.902 r_long_range_B_other 6.902 r_dihedral_angle_1_deg 6.471 r_scangle_other 3.327 r_mcangle_it 2.293 r_mcangle_other 2.293 r_scbond_it 2.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.814 r_dihedral_angle_3_deg 15.257 r_dihedral_angle_4_deg 13.434 r_long_range_B_refined 6.902 r_long_range_B_other 6.902 r_dihedral_angle_1_deg 6.471 r_scangle_other 3.327 r_mcangle_it 2.293 r_mcangle_other 2.293 r_scbond_it 2.101 r_scbond_other 2.101 r_angle_refined_deg 1.66 r_mcbond_it 1.431 r_mcbond_other 1.431 r_angle_other_deg 1.421 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4180 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing