3WUS | pdb_00003wus

Crystal Structure of the Vif-Binding Domain of Human APOBEC3F

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VOW	PDB ENTRY 3VOW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	8.5% PEG 20000, 2% Dioxane, 300mM L-Arginine HCl, 85mM Na BICINE, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.294	α = 90
b = 117.294	β = 90
c = 78.96	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	95	CCD	ADSC QUANTUM 315r		2012-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.54	101.58	99.9	0.107	36.1	10.9		20935

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.54	2.58	98.7

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 3VOW	2.54	50	19812	1069	99.78	0.20266	0.19979	0.2	0.25648	0.26	RANDOM	54.789

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]
1.39	0.69		1.39		-4.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.515
r_dihedral_angle_3_deg	19.567
r_dihedral_angle_4_deg	17.965
r_long_range_B_refined	11.135
r_long_range_B_other	11.134
r_dihedral_angle_1_deg	8.53
r_scangle_other	8.211
r_mcangle_other	7.023
r_mcangle_it	7.022
r_scbond_it	5.301
r_scbond_other	5.293
r_mcbond_it	4.565
r_mcbond_other	4.562
r_angle_refined_deg	1.863
r_angle_other_deg	0.895
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	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	3130
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SERGUI	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling