3LEF

Crystal structure of HIV epitope-scaffold 4E10_S0_1Z6NA_001

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z6N	Computationally-derived model of the epitope-scaffold, based on 1Z6N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	Na/K tartrate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.85	68.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.41	α = 90
b = 56.41	β = 90
c = 324.13	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	2007-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	48.3	93.7	0.086	9	8.4	13770	13770			56.3

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)
	2.3	2.38	91.5		0.373	3.9	6.83	1304

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Computationally-derived model of the epitope-scaffold, based on 1Z6N	2.3	46.78	13064	667	93.47	0.25978	0.25831	0.29042	RANDOM	49.573

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]
-0.22	-0.11		-0.22		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.951
r_dihedral_angle_4_deg	19.905
r_dihedral_angle_3_deg	16.259
r_dihedral_angle_1_deg	4.95
r_scangle_it	2.547
r_scbond_it	1.662
r_angle_refined_deg	1.146
r_mcangle_it	1.035
r_angle_other_deg	0.781
r_mcbond_it	0.666
r_symmetry_vdw_other	0.214
r_nbd_refined	0.203
r_nbd_other	0.203
r_xyhbond_nbd_refined	0.195
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.178
r_mcbond_other	0.133
r_symmetry_vdw_refined	0.098
r_nbtor_other	0.091
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1261
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	4

Software

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