3LH2 | pdb_00003lh2

Crystal structure of HIV epitope-scaffold 4E10_1VI7A_S0_002_N 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 epitope-scaffold Fv complex, with the Fv based on PDB ID 1TZG.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	Na acetate, imidazole, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.85	α = 90
b = 145.95	β = 92.43
c = 78.55	γ = 90

Symmetry
Space Group	P 1 21 1

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	2008-10-22	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	2.65	28.01	98.9	0.095	9.4	3.88	49017	49017			62.3

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)
	2.65	2.74	98.6		0.376	2.7	3.68	4883

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 Fv complex, with the Fv based on PDB ID 1TZG.	2.65	26.7	48955	48955	2478	98.53	0.22426	0.22173	0.23	0.27023	0.27	RANDOM	47.111

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]
-0.01		-0.01	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.776
r_dihedral_angle_4_deg	17.741
r_dihedral_angle_3_deg	15.617
r_dihedral_angle_1_deg	5.13
r_scangle_it	1.696
r_mcangle_it	1.052
r_scbond_it	1.039
r_angle_refined_deg	0.927
r_angle_other_deg	0.643
r_mcbond_it	0.585
r_symmetry_vdw_other	0.23
r_nbd_refined	0.208
r_nbd_other	0.208
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.188
r_symmetry_hbond_refined	0.161
r_symmetry_vdw_refined	0.132
r_xyhbond_nbd_other	0.101
r_nbtor_other	0.089
r_mcbond_other	0.067
r_chiral_restr	0.054
r_bond_refined_d	0.006
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_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	8997
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms

Software

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