6I21

Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A8B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29310-25% 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 = 106.389α = 90
b = 106.389β = 90
c = 67.486γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.567.481000.0710.074118.220.73651522.2
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)RedundancyNumber Unique Reflections (All)
11.51.541002.5952.7250.6441.321.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5A8B1.567.4834209188698.910.174760.173040.20501RANDOM26.378
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]
-0.39-0.19-0.391.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.594
r_sphericity_free27.908
r_dihedral_angle_3_deg14.797
r_dihedral_angle_4_deg14.495
r_sphericity_bonded8.616
r_dihedral_angle_1_deg6.054
r_long_range_B_refined3.884
r_long_range_B_other3.883
r_rigid_bond_restr2.754
r_scangle_other2.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.594
r_sphericity_free27.908
r_dihedral_angle_3_deg14.797
r_dihedral_angle_4_deg14.495
r_sphericity_bonded8.616
r_dihedral_angle_1_deg6.054
r_long_range_B_refined3.884
r_long_range_B_other3.883
r_rigid_bond_restr2.754
r_scangle_other2.7
r_scbond_other2.438
r_scbond_it2.437
r_mcangle_other2.319
r_mcangle_it2.317
r_angle_refined_deg2.006
r_mcbond_it1.828
r_mcbond_other1.814
r_angle_other_deg1.044
r_chiral_restr0.141
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms1057
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing