Experiment: 2QAD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RZK	YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG
experimental model	PDB	412D	YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG
experimental model	PDB	1RZG	YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	17-19% polyethylene glycol (PEG) 1500, 0.1 M Na cacodylate pH 6.5, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.6	α = 90
b = 53.021	β = 104.64
c = 225.326	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARRESEARCH		2004-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.3	50	67.8	0.133	0.133	9.1	3.1		25816		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.42	16.2		0.537	1.3	1.7	595

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG	3.3	20	38401	25600	1329	66.7	0.202	0.269	random	156

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]
-46.386		-20.021	16.91		29.475

RMS Deviations
Key	Refinement Restraint Deviation
f_angle_deg	1.092
f_bond_d	0.0054

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14497
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	490

Software

Software
Software Name	Purpose
PHENIX	refinement
AMoRE	phasing
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.