2NY2

HIV-1 gp120 Envelope Glycoprotein (T123C, T257S, S334A, S375W, G431C) Complexed with CD4 and Antibody 17b

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GC1	pdb entry 1GC1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	7.2% PEG 8000, 7.8% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.605	α = 90
b = 88.024	β = 90
c = 196.016	γ = 90

Symmetry
Space Group	P 2 2 21

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	MARMOSAIC 300 mm CCD		2005-03-03	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)	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	50	99.3	0.082	9.1	3.7	84379	83788		-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	2	2.07	94.4		0.374		3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1GC1	2	42.84	84461	75855	4062	94.62	0.19526	0.19379	0.22296	RANDOM	40.166

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]
			-0.06		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.529
r_dihedral_angle_4_deg	14.81
r_dihedral_angle_3_deg	12.812
r_dihedral_angle_1_deg	5.068
r_mcangle_it	1.232
r_scangle_it	0.969
r_angle_refined_deg	0.911
r_mcbond_it	0.715
r_scbond_it	0.597
r_nbtor_refined	0.319
r_symmetry_hbond_refined	0.318
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.199
r_symmetry_vdw_refined	0.144
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
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	7084
Nucleic Acid Atoms
Solvent Atoms	665
Heterogen Atoms	193

Software

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