3LHP | pdb_00003lhp

Crystal structure of HIV epitope-scaffold 4E10_D0_1ISEA_004_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	PEG 2000 MME, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.977	α = 90
b = 88.623	β = 90
c = 149.997	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	2008-03-10	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	2.7	29.54	96.2	0.102	7.1	3.45	19356	19356			69.7

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)
	2.7	2.8	85.5		0.405	2.2	2.86	1705

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.	2.7	28.99	19284	19284	980	96.02	0.24732	0.24267	0.25	0.33503	0.33	RANDOM	41.289

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]
-0.09			-0.16		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.397
r_dihedral_angle_3_deg	18.403
r_dihedral_angle_4_deg	14.274
r_dihedral_angle_1_deg	5.924
r_scangle_it	1.435
r_angle_refined_deg	1.132
r_scbond_it	0.956
r_angle_other_deg	0.806
r_mcangle_it	0.747
r_mcbond_it	0.541
r_nbd_refined	0.213
r_nbd_other	0.195
r_symmetry_vdw_other	0.192
r_symmetry_vdw_refined	0.187
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.104
r_nbtor_other	0.084
r_chiral_restr	0.051
r_mcbond_other	0.05
r_bond_refined_d	0.009
r_bond_other_d	0.007
r_xyhbond_nbd_other	0.004
r_gen_planes_refined	0.003
r_gen_planes_other	0.001
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	5112
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	4

Software

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