5BQC

Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 and sucrose octasulfate


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 Tris, pH 8.0, 0.15 M NaCl, 8% PEG8000
Crystal Properties
Matthews coefficientSolvent content
4.0369.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.136α = 90
b = 119.136β = 90
c = 119.151γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

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
1347.341000.130.0310.99914.619.610503
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)
133.181002.460.5480.1491.620.61648

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 REPLACEMENTTHROUGHOUT5BPB,5BPU347.34990457199.920.21750.21470.2676RANDOM113.96
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]
-3-1.5-39.74
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.748
r_sphericity_bonded22.406
r_mcangle_it7.397
r_mcbond_it5.283
r_mcbond_other5.28
r_angle_refined_deg1.181
r_rigid_bond_restr1.08
r_angle_other_deg0.935
r_chiral_restr0.05
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.748
r_sphericity_bonded22.406
r_mcangle_it7.397
r_mcbond_it5.283
r_mcbond_other5.28
r_angle_refined_deg1.181
r_rigid_bond_restr1.08
r_angle_other_deg0.935
r_chiral_restr0.05
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1759
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms83

Software

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