3MOA | pdb_00003moa

Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced Fab) with 17 aa gp41 MPER-derived peptide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.6	298	Reservoir; Hampton Research Crystal Screen 40 = 20% isopropanol, 20% PEG 4000, 100 mM Na citrate pH 5.6. Drop: 0.5 uL protein + 0.35 uL reservoir. Reservoir was NOT supplemented with 100 mM NaCl as in Ofek et al. 2004., VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.82	α = 90
b = 65.229	β = 90
c = 174.205	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	CCD	MARMOSAIC 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	2.3	43.7	100	0.062	15.4	7.3	30678	30678	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1TJI	2.3	43.683	0.19	30459	1986	99.47	0.1862	0.1839	0.176	0.2193	0.2077

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]
2.4653			0.1352		-2.6005

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.999
f_angle_d	1.348
f_chiral_restr	0.142
f_bond_d	0.027
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3506
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	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.