7PGX

Structure of dark-adapted AsLOV2 wild type


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V0U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62950.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
1.9837.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.5α = 90
b = 56.42β = 90
c = 66.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
1143.0793.10.99913.57.567933
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
111.060.51

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2v0u1.00143.06567871339493.1090.1160.11410.147212.143
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]
-0.1750.777-0.602
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.535
r_dihedral_angle_4_deg17.684
r_dihedral_angle_3_deg12.295
r_dihedral_angle_1_deg6.781
r_lrange_it2.95
r_lrange_other2.598
r_rigid_bond_restr2.492
r_scangle_it2.4
r_scangle_other2.399
r_scbond_other2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.535
r_dihedral_angle_4_deg17.684
r_dihedral_angle_3_deg12.295
r_dihedral_angle_1_deg6.781
r_lrange_it2.95
r_lrange_other2.598
r_rigid_bond_restr2.492
r_scangle_it2.4
r_scangle_other2.399
r_scbond_other2.25
r_scbond_it2.248
r_angle_refined_deg1.8
r_angle_other_deg1.471
r_mcangle_it1.128
r_mcangle_other1.127
r_mcbond_it0.935
r_mcbond_other0.863
r_symmetry_nbd_refined0.25
r_nbd_refined0.209
r_symmetry_xyhbond_nbd_refined0.197
r_symmetry_nbd_other0.186
r_nbtor_refined0.178
r_nbd_other0.172
r_xyhbond_nbd_refined0.161
r_chiral_restr0.111
r_symmetry_nbtor_other0.088
r_symmetry_xyhbond_nbd_other0.032
r_metal_ion_refined0.027
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1186
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing