3H3P

Crystal structure of HIV epitope-scaffold 4E10 Fv complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TZG	computationally-derived model of the Fv, based on 1TZG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	0.2 M calcium acetate, 8% PEG 8000, 0.1 M Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.4	α = 90
b = 92.4	β = 90
c = 272.79	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	107	IMAGE PLATE	RIGAKU RAXIS IV	Rigaku VariMax HR	2008-08-13	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)	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	2.7	69.02	98.6	0.104	7.5	4.56	19557	19557			63.6

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	2.7	2.8	99.6		0.347	2.9	4.29	8305

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	computationally-derived model of the Fv, based on 1TZG	2.7	60.08	18347	953	97.3	0.23171	0.2289	0.23	0.28697	0.29	RANDOM	59.2

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.999
r_dihedral_angle_4_deg	19.868
r_dihedral_angle_3_deg	16.597
r_dihedral_angle_1_deg	5.646
r_scangle_it	2.421
r_scbond_it	1.611
r_angle_refined_deg	1.109
r_mcangle_it	1.048
r_angle_other_deg	0.722
r_mcbond_it	0.7
r_symmetry_vdw_other	0.242
r_nbd_refined	0.236
r_nbd_other	0.227
r_symmetry_vdw_refined	0.2
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.173
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_other	0.122
r_mcbond_other	0.094
r_nbtor_other	0.088
r_metal_ion_refined	0.077
r_chiral_restr	0.061
r_bond_refined_d	0.008
r_bond_other_d	0.007
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3794
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	1

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling