6I24

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 DROP4.529310 - 25 % PEG 2K or 3K 0.1 M Na Acetate or Citrate 0.1 M NH4Cl

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.314α = 90
b = 106.314β = 90
c = 67.541γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9795DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4367.491000.0860.0890.99916.120.64199617
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)
11.431.471002.1142.2290.74119.7

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 REPLACEMENTTHROUGHOUT5A8B1.4367.4939822211099.840.186750.185880.20326RANDOM24.267
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]
0.140.070.14-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.807
r_dihedral_angle_3_deg15.217
r_dihedral_angle_4_deg12.714
r_dihedral_angle_1_deg5.854
r_long_range_B_refined5.62
r_long_range_B_other5.618
r_scangle_other2.224
r_angle_refined_deg1.93
r_scbond_it1.509
r_scbond_other1.508
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.807
r_dihedral_angle_3_deg15.217
r_dihedral_angle_4_deg12.714
r_dihedral_angle_1_deg5.854
r_long_range_B_refined5.62
r_long_range_B_other5.618
r_scangle_other2.224
r_angle_refined_deg1.93
r_scbond_it1.509
r_scbond_other1.508
r_mcangle_it1.325
r_mcangle_other1.324
r_angle_other_deg1.03
r_mcbond_it0.834
r_mcbond_other0.823
r_chiral_restr0.119
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms1057
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing