3LG7 | pdb_00003lg7

Crystal structure of HIV epitope-scaffold 4E10_S0_1EZ3A_002_C

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EZ3	Computationally-derived model of the epitope-scaffold, based on 1EZ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	Ammonium sulfate, bis Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.78	74.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.6	α = 90
b = 94.87	β = 90
c = 108.39	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	107	CCD	RIGAKU SATURN 944+	Rigaku Varimax HF	2008-05-09	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	2.5	28.82	99.5	0.107	6.6	4.53	33220	33220			66.7

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)
	2.5	2.59	96.8		0.429	2	3.78	3180

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	Computationally-derived model of the epitope-scaffold, based on 1EZ3	2.5	28.82	33123	33123	1672	99.39	0.25923	0.25702	0.27	0.30121	0.31	RANDOM	38.599

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]
0.06			-0.04		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.867
r_dihedral_angle_4_deg	21.723
r_dihedral_angle_3_deg	17.272
r_scangle_it	4.297
r_dihedral_angle_1_deg	3.952
r_scbond_it	2.96
r_mcbond_it	1.683
r_mcangle_it	1.667
r_angle_refined_deg	1.189
r_angle_other_deg	0.73
r_symmetry_vdw_other	0.357
r_nbd_refined	0.246
r_mcbond_other	0.222
r_symmetry_hbond_refined	0.199
r_nbtor_refined	0.198
r_nbd_other	0.194
r_xyhbond_nbd_refined	0.186
r_symmetry_vdw_refined	0.153
r_nbtor_other	0.089
r_chiral_restr	0.062
r_bond_refined_d	0.014
r_bond_other_d	0.005
r_gen_planes_refined	0.004
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3096
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	55

Software

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