4UQI | pdb_00004uqi

AP2 controls clathrin polymerization with a membrane-activated switch

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VGL	PDB ENTRY 2VGL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.2		18% PEG1000, 10MM NA/K PHOSPHATE PH 6.2, 200MM NACL, 4MM DTT, IP6

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.3	α = 90
b = 121.3	β = 90
c = 259.37	γ = 120

Symmetry
Space Group	P 31 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	CCD	ADSC CCD	MIRRORS	2010-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.79	97.37	99.9	0.07	21.9	10.9		55666		-3	74.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.86	100		0.86	3.2	11.2

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	PDB ENTRY 2VGL	2.79	97.37	52840	2824	99.92	0.20573	0.20292	0.2	0.2592	0.26	RANDOM	83.089

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]
0.22	0.11		0.22		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.545
r_dihedral_angle_3_deg	17.55
r_dihedral_angle_4_deg	16.775
r_dihedral_angle_1_deg	6.328
r_long_range_B_refined	3.907
r_long_range_B_other	3.907
r_scangle_other	2.817
r_mcangle_it	2.419
r_mcangle_other	2.419
r_angle_other_deg	2.152
r_scbond_it	1.82
r_scbond_other	1.82
r_mcbond_it	1.573
r_mcbond_other	1.573
r_angle_refined_deg	1.538
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.001
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	13849
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling