Experiment: 7KLC

Crystal structure of M4H2K1 Fab bound to HIV-1 BG505 gp120 core and to 17b Fab

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ONF	PDB entries 6ONF & 1GC1
experimental model	PDB	1GC1	PDB entries 6ONF & 1GC1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.1M Tris, pH 7, 1.825 M ammonium sulfate, 0.29 M lithium sulfate, 15% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 204.06	α = 90
b = 60.633	β = 90
c = 166.762	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER X 16M		2019-11-26	M	SINGLE WAVELENGTH

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

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	4.3	50	86.8	0.86	13	8.5		12843			138.69

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	4.3	4.37			0.39

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 6ONF & 1GC1	4.3	43.04	1.35	12392	569	83.96	0.3034	0.3019	0.302	0.3344	0.3349	169.05

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	18.1125
f_angle_d	0.8352
f_chiral_restr	0.0594
f_plane_restr	0.0049
f_bond_d	0.0038

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9420
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	282

Software

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