3G7A | pdb_00003g7a

HIV gp41 six-helix bundle composed of a chimeric alpha+alpha/beta-peptide analogue of the CHR domain in complex with an NHR domain alpha-peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F4Y	PDB entries 3F4Y, 3F50
experimental model	PDB	3F50	PDB entries 3F4Y, 3F50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.4 M lithium sulfate, 12% w/v PEG 8000, 20% v/v glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.043	α = 90
b = 57.043	β = 90
c = 186.314	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	BRUKER SMART 6000	confocal mirrors	2008-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.8	50	99.5	0.058	16.8	5.9	3100	3085

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	100		0.388	3.7	6.2

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	PDB entries 3F4Y, 3F50	2.8	25	2947	132	99.58	0.25425	0.25177	0.26	0.31083	0.35	RANDOM	32.413

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]
3.54	1.77		3.54		-5.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.576
r_dihedral_angle_3_deg	21.476
r_dihedral_angle_4_deg	14.274
r_mcangle_it	7.709
r_scangle_it	7.095
r_mcbond_it	5.461
r_dihedral_angle_1_deg	5.362
r_scbond_it	4.422
r_mcbond_other	2.261
r_angle_refined_deg	1.751
r_angle_other_deg	0.97
r_chiral_restr	0.081
r_bond_refined_d	0.018
r_bond_other_d	0.005
r_gen_planes_refined	0.004
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	574
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	27

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling