☰ Navigation Tabs
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 4.5 293 10 - 25 % PEG 2K or 3K
0.1 M Na Acetate or Citrate
0.1 M NH4Cl
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.314 α = 90 b = 106.314 β = 90 c = 67.541 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 6M 2017-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9795 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 1.43 67.49 100 0.086 0.089 0.999 16.1 20.6 41996 17
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 1.43 1.47 100 2.114 2.229 0.741 19.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5A8B 1.43 67.49 39822 2110 99.84 0.18675 0.18588 0.1952 0.20326 0.2126 RANDOM 24.267
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] 0.14 0.07 0.14 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.807 r_dihedral_angle_3_deg 15.217 r_dihedral_angle_4_deg 12.714 r_dihedral_angle_1_deg 5.854 r_long_range_B_refined 5.62 r_long_range_B_other 5.618 r_scangle_other 2.224 r_angle_refined_deg 1.93 r_scbond_it 1.509 r_scbond_other 1.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.807 r_dihedral_angle_3_deg 15.217 r_dihedral_angle_4_deg 12.714 r_dihedral_angle_1_deg 5.854 r_long_range_B_refined 5.62 r_long_range_B_other 5.618 r_scangle_other 2.224 r_angle_refined_deg 1.93 r_scbond_it 1.509 r_scbond_other 1.508 r_mcangle_it 1.325 r_mcangle_other 1.324 r_angle_other_deg 1.03 r_mcbond_it 0.834 r_mcbond_other 0.823 r_chiral_restr 0.119 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 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 1057 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing