4RFO

Crystal structure of the ADCC-Potent Antibody N60-I3 Fab in complex with HIV-1 Clade A/E gp120 and M48u1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	10-16% PEG 8000, 0.1 M Tris-HCl pH 8.5, 65 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.305	α = 90
b = 102.575	β = 90
c = 108.038	γ = 90

Symmetry
Space Group	P 21 21 2

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 325 mm CCD	RH coated flat mirror	2013-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.12709	SSRL	BL7-1

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	3.2	50	93.7	0.126	10.7	3.8	18694	17516

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	3.2	3.26	96		0.899	1.3	3.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3TNN FOR N60-I3, PDB ENTRY 4H8W FOR GP120, PDB ENTRY 4JZW FOR M48U1	3.2	36.013	16589	876	93.76	0.2226	0.21981	0.27702	RANDOM	116.914

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]
0.98			-8.03		7.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.936
r_dihedral_angle_4_deg	21.557
r_dihedral_angle_3_deg	20.34
r_long_range_B_refined	7.916
r_long_range_B_other	7.916
r_dihedral_angle_1_deg	7.834
r_scangle_other	3.304
r_mcangle_it	3.101
r_mcangle_other	3.072
r_scbond_it	2.226
r_scbond_other	1.971
r_mcbond_it	1.813
r_mcbond_other	1.813
r_angle_refined_deg	1.411
r_angle_other_deg	0.836
r_chiral_restr	0.08
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	6042
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	126

Software

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