5M5V

Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 2)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293200 nL protein:peptide (20 mg/mL NTD and 3.6 mM peptide) plus 400 nL reservoir equilibrated against a 80 uL reservoir of 1.75 M sodium malonate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.6466.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.9α = 90
b = 131.23β = 115.86
c = 78.45γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FKB mirrors2013-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

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
11.9639.294.60.0810.9967.22.579976
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)
11.96295.90.5810.5631.52.3

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 REPLACEMENTTHROUGHOUT1C9I1.9639.279976422494.420.170370.169140.19343RANDOM33.338
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]
0.01-0.510.210.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg14.392
r_dihedral_angle_3_deg14.112
r_long_range_B_refined8.246
r_long_range_B_other8.245
r_dihedral_angle_1_deg7.233
r_scangle_other3.907
r_mcangle_it2.805
r_mcangle_other2.805
r_scbond_it2.494
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg14.392
r_dihedral_angle_3_deg14.112
r_long_range_B_refined8.246
r_long_range_B_other8.245
r_dihedral_angle_1_deg7.233
r_scangle_other3.907
r_mcangle_it2.805
r_mcangle_other2.805
r_scbond_it2.494
r_scbond_other2.494
r_angle_refined_deg1.917
r_mcbond_it1.767
r_mcbond_other1.767
r_angle_other_deg1.096
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms5862
Nucleic Acid Atoms
Solvent Atoms583
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing