3HI1

Structure of HIV-1 gp120 (core with V3) in Complex with CD4-Binding-Site Antibody F105

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BBD	PDB ENTRIES 1BBD, 1BBJ
experimental model	PDB	1BBJ	PDB ENTRIES 1BBD, 1BBJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	293	16% PEG 6000, 8% 2-PROPANOL, 0.2M AMMONIUM SULFATE, 0.1M HEPES, PH 7.5, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.08	69.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 412.403	α = 90
b = 412.403	β = 90
c = 83.206	γ = 120

Symmetry
Space Group	H 3 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 300 mm CCD		2005-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	2.9	50		0.123	0.085	13.1	4.4		48590

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	2.9	2.98			0.456	0.413	1.21	1.5

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 ENTRIES 1BBD, 1BBJ	2.9	43.48	42563	2247	75.5	0.204	0.202	0.243	RANDOM	119.9

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]
1.02	0.51		1.02		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.958
r_dihedral_angle_4_deg	17.851
r_dihedral_angle_3_deg	15.623
r_dihedral_angle_1_deg	6.085
r_mcangle_it	2.445
r_mcbond_it	1.371
r_scangle_it	1.213
r_angle_refined_deg	1.154
r_scbond_it	0.71
r_nbtor_refined	0.336
r_nbd_refined	0.259
r_symmetry_vdw_refined	0.251
r_symmetry_hbond_refined	0.215
r_xyhbond_nbd_refined	0.198
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11214
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	378

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling