5BQE

Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 -Methylated form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BPB5BPB,5BPU
experimental modelPDB 5BPU5BPB,5BPU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.1 M Bicine, pH 9.0, 10% PEG6000
Crystal Properties
Matthews coefficientSolvent content
3.3463.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.92α = 90
b = 98.92β = 90
c = 120.42γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
12.349.4698.90.1030.0450.99810.762681648.29
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3897.21.2120.5610.2881.45.62514

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5BPB,5BPU2.349.461.3426803134598.510.19780.19660.2211Random selection63.08
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.34
f_angle_d0.927
f_chiral_restr0.039
f_bond_d0.004
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2557
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms39

Software

Software
Software NamePurpose
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction