3Q6F | pdb_00003q6f

Crystal structure of Fab of human mAb 2909 specific for quaternary neutralizing epitope of HIV-1 gp120

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.8	296	14% PEG 8000, 0.1M HEPES, pH6.8, 0.1M glycine, and 8% ethylene glycol, under the oil, temperature 296K, EVAPORATION

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.504	α = 90
b = 178.504	β = 90
c = 218.9	γ = 120

Symmetry
Space Group	P 32 2 1

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	MAR scanner 300 mm plate		2010-02-18	M	SINGLE WAVELENGTH
2	1	x-ray
3	1	x-ray
4	1	x-ray

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03321	APS	23-ID-B
2	SYNCHROTRON	NSLS BEAMLINE X6A	1.0	NSLS	X6A
3	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID
4	SYNCHROTRON	NSLS BEAMLINE X4C	1.0	NSLS	X4C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2,3,4	3	50	99.5				66903

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3,4	3	3.05	78.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	3.192	46.653	0.19	66903	66876	3391	99.25	0.2013	0.199	0.1947	0.2429	0.2385

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]
-2.7791			-2.7791		5.5582

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.868
f_angle_d	1.234
f_chiral_restr	0.079
f_bond_d	0.01
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20042
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	42

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.