2NY7 | pdb_00002ny7

HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.955	α = 90
b = 101.955	β = 90
c = 298.294	γ = 120

Symmetry
Space Group	P 65 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	MARMOSAIC 300 mm CCD		2003-10-13	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	2.3	50	97.2	0.096	9.8	8.8	41973	40798		-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	2.3	2.38	77.5		0.755		2.3

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 entries 1HZH, 1GC1	2.3	49.45	40751	36114	1890	93.26	0.19601	0.19291	0.19	0.25503	0.25	RANDOM	62.345

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]
0.04	0.02		0.04		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.691
r_dihedral_angle_4_deg	17.829
r_dihedral_angle_3_deg	14.657
r_scangle_it	7.281
r_scbond_it	5.296
r_dihedral_angle_1_deg	5.18
r_mcangle_it	3.235
r_mcbond_it	2.174
r_angle_refined_deg	0.852
r_nbtor_refined	0.325
r_xyhbond_nbd_refined	0.238
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.216
r_symmetry_hbond_refined	0.205
r_chiral_restr	0.056
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
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	5687
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	182

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
HKL-2000	data scaling
AMoRE	phasing