3QEG

Crystal structure of human N12-i2 Fab, an ADCC and neutralizing anti-HIV-1 Env antibody

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	0.01 M Ni (II) chloride hexahydrate, 0.1 M Tris HCl, pH 8.5, 20% Polyethylene glycol monomethyl ether 2,000, , VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.906	α = 90
b = 78.906	β = 90
c = 315.147	γ = 120

Symmetry
Space Group	P 61 2 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	ADSC QUANTUM 315		2010-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.979464	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	68.335	99	0.094	0.065	40	20.2	43646	43613	1	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	99.7		0.795	0.618	2.5	15.2	4255

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RZ8	1.95	20	2	2946	41215	2189	99.59	0.20483	0.20483	0.20316	0.23612	RANDOM	41.489

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]
1.74	0.87		1.74		-2.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.929
r_dihedral_angle_4_deg	19.33
r_dihedral_angle_3_deg	15.239
r_dihedral_angle_1_deg	7.099
r_scangle_it	4.658
r_scbond_it	3.01
r_mcangle_it	1.849
r_angle_refined_deg	1.794
r_mcbond_it	1.053
r_chiral_restr	0.143

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.929
r_dihedral_angle_4_deg	19.33
r_dihedral_angle_3_deg	15.239
r_dihedral_angle_1_deg	7.099
r_scangle_it	4.658
r_scbond_it	3.01
r_mcangle_it	1.849
r_angle_refined_deg	1.794
r_mcbond_it	1.053
r_chiral_restr	0.143
r_bond_refined_d	0.02
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3261
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.