4RFN | pdb_00004rfn

Crystal structure of ADCC-potent Rhesus macaque ANTIBODY JR4 in complex with HIV-1 CLADE A/E GP120 and M48

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RFE	PDB entry 4RFE for JR4, PDB entry 4H8W for gp120, PDB entry 2I5Y for M48
experimental model	PDB	4H8W	PDB entry 4RFE for JR4, PDB entry 4H8W for gp120, PDB entry 2I5Y for M48
experimental model	PDB	2I5Y	PDB entry 4RFE for JR4, PDB entry 4H8W for gp120, PDB entry 2I5Y for M48

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.255	α = 90
b = 77.827	β = 114.26
c = 127.587	γ = 90

Symmetry
Space Group	P 1 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 315	RH coated flat mirror	2012-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.1271	SSRL	BL7-1

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	3.17	50	99.8	0.252	6.9	3.7		33553

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	3.17	3.23	100		0.871	1.9	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 4RFE for JR4, PDB entry 4H8W for gp120, PDB entry 2I5Y for M48	3.21	45	30928	1643	99.72	0.27623	0.27335	0.27	0.33226	0.33	RANDOM	94.681

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]
-7.72		1.18	0.49		4.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.234
r_dihedral_angle_3_deg	16.792
r_dihedral_angle_4_deg	12.472
r_dihedral_angle_1_deg	6.392
r_scbond_it	2.103
r_long_range_B_refined	1.668
r_long_range_B_other	1.668
r_angle_refined_deg	1.148
r_mcangle_it	0.981
r_mcangle_other	0.87
r_angle_other_deg	0.794
r_scangle_other	0.767
r_mcbond_it	0.541
r_mcbond_other	0.54
r_scbond_other	0.451
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12086
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	252

Software

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