5F6J | pdb_00005f6j

Crystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rhesus Macaque in Complex with HIV-1 gp120 Core

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LST	HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H
experimental model	PDB	5F6H	HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	1.5M ammonium sulfate and 100 mM Tris, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
5.1	75.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.902	α = 90
b = 162.902	β = 90
c = 229.854	γ = 120

Symmetry
Space Group	P 64

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		2015-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97916	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	6.63	141.08	93.2	0.273	0.312	0.146	7.5	6.7		6058

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	6.63	6.8	94.1		1.1	6.6

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	HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H	6.63	141.08	5756	302	93.24	0.2585	0.256	0.26	0.3046	0.3	RANDOM	276.625

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]
-1.41	-0.71		-1.41		4.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.348
r_dihedral_angle_3_deg	18.676
r_mcangle_it	17.615
r_dihedral_angle_4_deg	16.746
r_mcbond_it	9.979
r_scbond_it	9.757
r_dihedral_angle_1_deg	6.457
r_angle_refined_deg	1.389
r_chiral_restr	0.084
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.348
r_dihedral_angle_3_deg	18.676
r_mcangle_it	17.615
r_dihedral_angle_4_deg	16.746
r_mcbond_it	9.979
r_scbond_it	9.757
r_dihedral_angle_1_deg	6.457
r_angle_refined_deg	1.389
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11572
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building

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.