4YBL | pdb_00004ybl

Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 in complex with the ADCC mediating ANTI-HIV-1 antibody A32

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TNM	3TNM and 4RQH
experimental model	PDB	4RQH	3TNM and 4RQH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	18-22% PEG 6000 or 8000 0.1 M Tris-HCl pH 8.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.742	α = 90
b = 208.209	β = 90
c = 73.22	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	ADSC QUANTUM 315		2014-11-28	M	SINGLE WAVELENGTH
2	2	x-ray	100	PIXEL	PSI PILATUS 6M		2015-01-23	M	SINGLE WAVELENGTH
3	3	100

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.12789	SSRL	BL7-1
2	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

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	3.1	50	93.2	0.186	14.6	8.3	21415	19959

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	3.1	3.15	96.8		0.955	1.3	8.3

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	3TNM and 4RQH	3.1	50	18913	1021	91.54	0.2346	0.23178	0.23	0.28937	0.28	RANDOM	94.206

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]
-0.92			-0.36		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.47
r_dihedral_angle_3_deg	17.248
r_dihedral_angle_4_deg	13.927
r_dihedral_angle_1_deg	8.57
r_long_range_B_refined	4.03
r_long_range_B_other	4.03
r_angle_refined_deg	1.527
r_mcangle_it	1.486
r_mcangle_other	1.486
r_scangle_other	1.103
r_angle_other_deg	1.016
r_mcbond_it	0.814
r_mcbond_other	0.814
r_scbond_it	0.59
r_scbond_other	0.59
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
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	8470
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
CNS	refinement
PHASER	phasing
HKL-2000	data scaling