3RBB | pdb_00003rbb

HIV-1 NEF protein in complex with engineered HCK SH3 domain

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.1 M Hepes, 8% ethylene glycol, 22% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.19	α = 90
b = 90.88	β = 90
c = 169.53	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD		2009-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.977032	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.35	48	99.5	22.18		28573	28573	-3	-3

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	2.35	2.4	98.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1EFN	2.35	47.99	27143	27143	1429	100	0.20589	0.20379	0.2092	0.24513	0.2524	RANDOM	46.806

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]
0.87			2.58		-3.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.616
r_dihedral_angle_4_deg	19.43
r_dihedral_angle_3_deg	16.141
r_dihedral_angle_1_deg	5.926
r_scangle_it	3.194
r_scbond_it	1.966
r_mcangle_it	1.364
r_angle_refined_deg	1.329
r_mcbond_it	0.739
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3120
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	8

Software

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