3BQL

Structure of a chondroitin sulphate binding DBL3X domain from a var2csa encoded PfEMP1 protein

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	25% PEG 4K, 20mM HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.576	α = 90
b = 86.99	β = 90
c = 92.659	γ = 90

Symmetry
Space Group	P 21 21 21

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 1		2007-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.06	Diamond	I04

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	1.8	62.99	97.7	0.083	0.083	11.6	3.8		30158	2	2	27.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	100		0.348	0.348	5.4	7.2	11894

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	2	46.32	2	2	22216	1202	99.97	0.22486	0.22244	0.27081	RANDOM	33.29

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]
0.17			-0.2		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.306
r_dihedral_angle_3_deg	15.157
r_dihedral_angle_4_deg	12.828
r_dihedral_angle_1_deg	7.904
r_scangle_it	2.904
r_scbond_it	1.813
r_mcangle_it	1.563
r_angle_refined_deg	1.137
r_mcbond_it	0.922
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.306
r_dihedral_angle_3_deg	15.157
r_dihedral_angle_4_deg	12.828
r_dihedral_angle_1_deg	7.904
r_scangle_it	2.904
r_scbond_it	1.813
r_mcangle_it	1.563
r_angle_refined_deg	1.137
r_mcbond_it	0.922
r_nbtor_refined	0.299
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.167
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2732
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.