2QSC

Crystal structure analysis of anti-HIV-1 V3-Fab F425-B4e8 in complex with a V3-peptide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	298	PEG 8000, pH 6.0, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.912	α = 90
b = 39.858	β = 108.5
c = 97.96	γ = 90

Symmetry
Space Group	P 1 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	CCD	MARMOSAIC 325 mm CCD	Rh coated flat mirror	2007-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.8	50	99	0.102	12.6	3.7		15169		-3	60.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.87	94.6		0.476	2.3	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.8	50	15169	755	98.85	0.222	0.219	0.264	RANDOM	49.742

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]
-0.75		1.78	3.43		-1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.385
r_dihedral_angle_3_deg	14.64
r_dihedral_angle_4_deg	10.55
r_dihedral_angle_1_deg	5.25
r_angle_refined_deg	0.946
r_scangle_it	0.82
r_scbond_it	0.435
r_nbtor_refined	0.298
r_mcangle_it	0.267
r_symmetry_vdw_refined	0.196

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.385
r_dihedral_angle_3_deg	14.64
r_dihedral_angle_4_deg	10.55
r_dihedral_angle_1_deg	5.25
r_angle_refined_deg	0.946
r_scangle_it	0.82
r_scbond_it	0.435
r_nbtor_refined	0.298
r_mcangle_it	0.267
r_symmetry_vdw_refined	0.196
r_nbd_refined	0.172
r_mcbond_it	0.147
r_xyhbond_nbd_refined	0.106
r_metal_ion_refined	0.067
r_chiral_restr	0.06
r_symmetry_hbond_refined	0.028
r_bond_refined_d	0.005
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3353
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.