Experiment: 5UKP

Structure of unliganded anti-gp120 CD4bs antibody DH522.1 Fab

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4QHK	The starting model was a hybrid of the heavy chain from CH103UCA Fab (PDB 4QHK) with the light chain from A32 (PDB 3TNM).
experimental model	PDB	3TNM	The starting model was a hybrid of the heavy chain from CH103UCA Fab (PDB 4QHK) with the light chain from A32 (PDB 3TNM).

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M HEPES pH 7.5, 30% 1,2-propanediol, 20% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.682	α = 90
b = 70.682	β = 90
c = 169.835	γ = 120

Symmetry
Space Group	P 31 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	93	CCD	MARMOSAIC 300 mm CCD		2015-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2	50	99.7	0.077	18.4	5.6		33888

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	The starting model was a hybrid of the heavy chain from CH103UCA Fab (PDB 4QHK) with the light chain from A32 (PDB 3TNM).	2	41.562	32746	1929	96.39	0.1942	0.1916	0.1918	0.2361	0.2328

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	12.95
f_angle_d	1.182
f_chiral_restr	0.045
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3216
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms

Software

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