9CF6 | pdb_00009cf6

Germline-targeting HIV-1 gp120 engineered outer domain eODgt8 in complex with Fab eOD-CL02.1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IES
experimental model	PDB	6WFY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M magnesium nitrate, 20% Peg3350, 15% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.039	α = 90
b = 72.601	β = 107.52
c = 93.817	γ = 90

Symmetry
Space Group	C 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	PIXEL	DECTRIS PILATUS 6M		2019-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.7	39.883	98.3	0.158	0.174	0.072	0.988	7.7	5.6		18286		-3	52.94

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.83	99.4		1.04	1.15	0.473	0.753	1.6	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.7	39.883	18169	870	97.369	0.277	0.2759	0.273	0.3061	0.2893	53.215

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]
1.514		-4.092	-2.391		2.885

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.729
r_dihedral_angle_3_deg	11.71
r_lrange_it	7.464
r_dihedral_angle_1_deg	5.678
r_dihedral_angle_2_deg	3.833
r_mcangle_it	3.187
r_scangle_it	2.818
r_mcbond_it	1.789
r_scbond_it	1.609
r_angle_refined_deg	1.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.729
r_dihedral_angle_3_deg	11.71
r_lrange_it	7.464
r_dihedral_angle_1_deg	5.678
r_dihedral_angle_2_deg	3.833
r_mcangle_it	3.187
r_scangle_it	2.818
r_mcbond_it	1.789
r_scbond_it	1.609
r_angle_refined_deg	1.131
r_nbtor_refined	0.307
r_symmetry_xyhbond_nbd_refined	0.286
r_symmetry_nbd_refined	0.241
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.068
r_bond_refined_d	0.004
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4430
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

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.