5M5U | pdb_00005m5u

Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C9I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	400 nL protein:peptide mix (14 mg/mL NTD and 3.4 mM) plus 200 nL reservoir equilibrated against a 80 uL reservoir of 1.21 M sodium malonate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.23	α = 90
b = 131.19	β = 115.61
c = 77.87	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F	KB mirrors	2013-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.15	48.8	99.7	0.101	0.996	9.6	4.5		63339

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)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	99		0.93	0.501	1.5	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1C9I	2.15	48.37	63339	3381	99.71	0.17696	0.17536	0.18	0.20704	0.21	RANDOM	40.846

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]
		0.66	-1.73		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.558
r_dihedral_angle_4_deg	18.695
r_dihedral_angle_3_deg	14.575
r_long_range_B_refined	8.935
r_long_range_B_other	8.934
r_dihedral_angle_1_deg	7.232
r_scangle_other	4.465
r_mcangle_it	3.299
r_mcangle_other	3.298
r_scbond_it	2.874
r_scbond_other	2.874
r_mcbond_it	2.144
r_mcbond_other	2.119
r_angle_refined_deg	1.897
r_angle_other_deg	1.032
r_chiral_restr	0.11
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.005
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 Atoms	Number
Protein Atoms	5822
Nucleic Acid Atoms
Solvent Atoms	437
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing