6FZN

SMURFP-Y56R mutant in complex with biliverdin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82922% v/v 1,4-dioxane, 0.1 M Tris pH 8.0, 15% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
1.9737.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.55α = 90
b = 57.96β = 105.04
c = 52.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.000009SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.55098.60.0880.99910.836.9845279.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.57980.80.8111.997

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.550799146198.670.214750.212110.26258RANDOM70
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]
5.75-3.19-1.56-2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.547
r_dihedral_angle_4_deg15.522
r_dihedral_angle_3_deg15.298
r_long_range_B_other7.457
r_long_range_B_refined7.455
r_dihedral_angle_1_deg5.478
r_scangle_other4.761
r_mcangle_other4.623
r_mcangle_it4.622
r_mcbond_it2.864
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.547
r_dihedral_angle_4_deg15.522
r_dihedral_angle_3_deg15.298
r_long_range_B_other7.457
r_long_range_B_refined7.455
r_dihedral_angle_1_deg5.478
r_scangle_other4.761
r_mcangle_other4.623
r_mcangle_it4.622
r_mcbond_it2.864
r_scbond_it2.841
r_mcbond_other2.84
r_scbond_other2.839
r_angle_refined_deg1.561
r_angle_other_deg0.964
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.007
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2102
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing