3DRQ | pdb_00003drq

Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 FP-MPER Hyb3K construct 514GIGALFLGFLGAAGS528KK-Ahx-655KNEQELLELDKWASLWN671 soaked in PEG/2-propanol solution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D0L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	Crystals grown in 0.1 M Nacitrate pH 5.6, 1.6 M ammonium sulfate, 0.01% Tween-20 and soaked for 36h in 0.1 M Nacitrate pH 5.6, 16% PEG 4K, 16% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.5	α = 90
b = 76.6	β = 90
c = 94.2	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2007-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

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	2	20	97.9	0.098		3.5	31694	31016			16.2

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	1.99	2.11	96.1		0.454		1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	3D0L	2	19.9	31694	31016	1550	97.7	0.227	0.227	0.22	0.254	0.25	RANDOM	26.5

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]
1.78			0.31		-2.1

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	29
c_scangle_it	2.78
c_mcangle_it	2.03
c_scbond_it	1.99
c_angle_deg	1.7
c_mcbond_it	1.26
c_improper_angle_d	1.02
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3327
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	6

Software

Software
Software Name	Purpose
CNS	refinement
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

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.