2B4C | pdb_00002b4c

Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	293	ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.50

Crystal Properties
Matthews coefficient	Solvent content
3.28	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 225.993	α = 90
b = 225.993	β = 90
c = 97.968	γ = 120

Symmetry
Space Group	P 6 2 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	MARRESEARCH		2004-03-12	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.3	20	86.6	0.082	0.082	26.2	9.6		19372		-3

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	3.3	3.42	20.9		0.505	1.3	3.1

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 1RHH AND 1RZK	3.3	20	22571	19364	1920	86.2	0.319	0.319	0.28	0.349	0.31	RANDOM	126.2

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]
11.12	19.38		11.12		-22.25

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.3
c_angle_deg	0.98
c_improper_angle_d	0.64
c_bond_d	0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7396
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	121

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing