4GAG | pdb_00004gag

Structure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 412-423)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	18% PEG 8K, 0.1M TrisHCl, 0.2M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.649	α = 90
b = 56.903	β = 113.9
c = 81.802	γ = 90

Symmetry
Space Group	C 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	RIGAKU SATURN 944		2010-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.8	50	98.28			49991	49991	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	23.11	2	49991	46640	2492	98.28	0.17935	0.17765	0.1769	0.21092	0.2103	RANDOM	24.877

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]
-1.21		-0.33	-0.11		1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.552
r_dihedral_angle_4_deg	22.4
r_dihedral_angle_3_deg	13.296
r_dihedral_angle_1_deg	7.197
r_scangle_it	5.474
r_scbond_it	3.455
r_mcangle_it	2.466
r_angle_refined_deg	2.211
r_mcbond_it	1.469
r_chiral_restr	0.196
r_bond_refined_d	0.028
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3384
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling