3LF6 | pdb_00003lf6

Crystal structure of HIV epitope-scaffold 4E10_1XIZA_S0_001_N

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	DI-AMMONIUM PHOSPHATE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.211	α = 90
b = 81.975	β = 90
c = 94.219	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	IMAGE PLATE	RIGAKU RAXIS IV++	Rigaku Varimax HR	2008-01-03	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	1.9	49.21	97.5	0.057	17.2	4.43		30053			22.3

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)
	1.9	1.97	95.2		0.341	2.6	4.4	2886

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 epitope-scaffold, based on 1XIZ	1.9	31.5	26499	1420	90.63	0.22615	0.22324	0.23	0.27917	0.29	RANDOM	32.353

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]
-0.4			0.07		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.211
r_dihedral_angle_4_deg	14.779
r_dihedral_angle_3_deg	12.843
r_dihedral_angle_1_deg	5.156
r_scangle_it	2.345
r_scbond_it	1.686
r_mcangle_it	1.173
r_angle_refined_deg	1.056
r_mcbond_it	0.763
r_angle_other_deg	0.743
r_symmetry_vdw_other	0.354
r_symmetry_hbond_refined	0.266
r_xyhbond_nbd_refined	0.218
r_nbd_other	0.208
r_nbd_refined	0.205
r_nbtor_refined	0.186
r_mcbond_other	0.179
r_nbtor_other	0.087
r_chiral_restr	0.061
r_symmetry_vdw_refined	0.053
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	2448
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	15

Software

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