3U91 | pdb_00003u91

Structural Determinants of Trimerization Specificity in HIV-1 gp41 Protein

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AIK	PDB ENTRY 1AIK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	20% Jeffamine M600, 0.1M MES, 25mM Cesium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.308	α = 90
b = 45.308	β = 90
c = 42.16	γ = 120

Symmetry
Space Group	P 3 2 1

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	ADSC QUANTUM 4		2005-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.9676	NSLS	X4A

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	1.45	42.14	99.8	0.065	9.1	8.8		9173

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	1.45	1.5	99.8		0.467	6.4	8.8

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	PDB ENTRY 1AIK	1.45	42.14	9173	8256	917	99.85	0.19585	0.19191	0.19	0.23341	0.23	RANDOM	26.142

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]
0.62	0.31		0.62		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.213
r_dihedral_angle_3_deg	12.035
r_dihedral_angle_4_deg	7.733
r_dihedral_angle_1_deg	4.226
r_scangle_it	3.846
r_scbond_it	2.362
r_mcangle_it	1.42
r_angle_refined_deg	1.138
r_mcbond_it	0.784
r_nbtor_refined	0.301
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.138
r_xyhbond_nbd_refined	0.13
r_symmetry_hbond_refined	0.103
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	255
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	13

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling