7KMD | pdb_00007kmd

Crystal structure of a HIV-1 clade C isolate Du172.17 HR1.R4.664 Env trimer in complex with human Fabs PGT124 and 35O22

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CEZ	PDB entries 5CEZ, 4TOY, 4R26
experimental model	PDB	4TOY	PDB entries 5CEZ, 4TOY, 4R26
experimental model	PDB	4R26	PDB entries 5CEZ, 4TOY, 4R26

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.1M Tris pH=8.4, 25%(v/v) PEG400

Crystal Properties
Matthews coefficient	Solvent content
4.39	72.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.016	α = 90
b = 127.016	β = 90
c = 316.538	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2019-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	3.39	50	97.6	0.85	8.6	6.4		38788			92.5907504709

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.46			0.45

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	FREE R-VALUE	PDB entries 5CEZ, 4TOY, 4R26	3.39228580771	49.5301719699	1.33790597134	38200	1917	95.7753541432	0.244439177019	0.241970008729	0.24	0.29172476334	0.29	113.176596028

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.312812868
f_angle_d	1.48301479719
f_chiral_restr	0.118800754756
f_bond_d	0.00409734705206
f_plane_restr	0.0038837308944

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11318
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	715

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Coot	model building
HKL-2000	data scaling
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.