4HQX

CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MJG	CHAIN A of 3MJG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	289	PROPLEX E1: 0.1 M MAGNESIUM ACETATE, 0.1 M SODIUM ACETATE PH 4.5, 8% PEG 8000, VAPOR DIFFUSION, TEMPERATURE 289K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.43	α = 90
b = 59.43	β = 90
c = 168.16	γ = 90

Symmetry
Space Group	P 41 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	CCD	ADSC QUANTUM 315r		2011-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979176	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	19.675	97.2	0.064	19.29			13750		-3	50.08

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	2.3	2.36	98.4		0.572	2.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	CHAIN A of 3MJG	2.3	19.675	13750	679		0.241	0.239	0.279	RANDOM	42.86

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]
2.33			2.33		-4.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.582
r_dihedral_angle_4_deg	25.856
r_dihedral_angle_3_deg	14.965
r_dihedral_angle_1_deg	6.101
r_angle_refined_deg	2.005
r_chiral_restr	0.1
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	738
Nucleic Acid Atoms	553
Solvent Atoms	58
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement

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.