7PGZ

Structure of dark-adapted AsLOV2 Q513L


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62980.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
1.9235.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.61α = 90
b = 54.55β = 90
c = 66.46γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2019-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.7999BESSY14.2

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
10.942.1799113.87.295419
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)
10.90.9597.60.3710.996.9

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-VALUE2V0U0.942.16595415477198.9340.1160.1150.139310.258
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]
-0.210.337-0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.134
r_dihedral_angle_4_deg16.693
r_dihedral_angle_3_deg14.158
r_dihedral_angle_1_deg7.119
r_lrange_it2.41
r_rigid_bond_restr2.278
r_lrange_other2.243
r_angle_refined_deg1.987
r_scangle_it1.947
r_scangle_other1.946
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.134
r_dihedral_angle_4_deg16.693
r_dihedral_angle_3_deg14.158
r_dihedral_angle_1_deg7.119
r_lrange_it2.41
r_rigid_bond_restr2.278
r_lrange_other2.243
r_angle_refined_deg1.987
r_scangle_it1.947
r_scangle_other1.946
r_scbond_other1.719
r_scbond_it1.718
r_angle_other_deg1.479
r_mcangle_it1.071
r_mcangle_other1.07
r_mcbond_it0.863
r_mcbond_other0.856
r_nbd_refined0.34
r_symmetry_nbd_refined0.31
r_nbd_other0.25
r_symmetry_nbd_other0.213
r_xyhbond_nbd_refined0.208
r_symmetry_xyhbond_nbd_refined0.196
r_nbtor_refined0.189
r_chiral_restr0.102
r_symmetry_nbtor_other0.088
r_symmetry_xyhbond_nbd_other0.024
r_xyhbond_nbd_other0.015
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1185
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms119

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing