Experiment: 3JWO

Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3JWD	pdb entry 3JWD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	5.3% PEG8000, 0.2M Calcium acetate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 190	α = 90
b = 190	β = 90
c = 103.302	γ = 90

Symmetry
Space Group	P 41 21 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	IMAGE PLATE	MAR scanner 300 mm plate		2009-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

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	3.5	50	87.4	0.217	8.06	2.3		20271	1	1

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	3.5	3.63	41.8		0.553	1.3	1.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entry 3JWD	3.51	41.09	0.11	20271	1842	83.8	0.258	0.257	0.2521	0.273	0.2685	141.66

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]
-21.939			-21.939		43.878

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.425
f_angle_d	0.861
f_chiral_restr	0.051
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7433
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	164

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection