9CF7 | pdb_00009cf7

Germline-targeting HIV-1 gp120 engineered outer domain eODgt8 in complex with Fab eOD-PL01.1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IES
experimental model	PDB	7N3H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2M potassium dihydrogen phosphate, 20% Peg3350

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.767	α = 90
b = 166.767	β = 90
c = 100.693	γ = 120

Symmetry
Space Group	P 64 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	PIXEL	DECTRIS PILATUS 6M		2019-06-13	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	3.55	38.55	99.4	0.26	0.274	0.087	0.997	9.1	9.5		10327		-3	166

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	3.55	3.89	99.9		3.1	3.25	1	0.613	1	9.9

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	3.55	38.55	9825	447	94.163	0.267	0.2654	0.2692	0.2994	0.3097	162.615

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]
1.112	0.556		1.112		-3.606

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.397
r_dihedral_angle_6_deg	12.382
r_lrange_it	11.897
r_dihedral_angle_1_deg	6.478
r_mcangle_it	5.699
r_scangle_it	5.203
r_dihedral_angle_2_deg	4.068
r_mcbond_it	3.176
r_scbond_it	2.859
r_angle_refined_deg	0.994

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.397
r_dihedral_angle_6_deg	12.382
r_lrange_it	11.897
r_dihedral_angle_1_deg	6.478
r_mcangle_it	5.699
r_scangle_it	5.203
r_dihedral_angle_2_deg	4.068
r_mcbond_it	3.176
r_scbond_it	2.859
r_angle_refined_deg	0.994
r_nbtor_refined	0.303
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.168
r_symmetry_nbd_refined	0.132
r_symmetry_xyhbond_nbd_refined	0.113
r_chiral_restr	0.067
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4480
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.