3BQK | pdb_00003bqk

Structure of a chondroitin sulphate binding DBL3X from a var2csa encoded PfEMP1 protein in complex with sulphate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	20% PEG 4K, 20mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2	38.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.258	α = 90
b = 86.555	β = 90
c = 92.33	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		CCD	ADSC QUANTUM 1		2007-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.979	ESRF	ID14-4

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	63	99.8	0.101	0.101	14.5	7		31419	2	2	25.9

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	1.8	1.9	100		0.791	0.791	2.2	7.1	4507

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	46.18	29784	1575	99.78	0.23382	0.23093	0.25	0.28647	0.3	RANDOM	20.148

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]
0.04			-0.2		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.609
r_dihedral_angle_3_deg	14.258
r_dihedral_angle_4_deg	10.69
r_dihedral_angle_1_deg	7.811
r_scangle_it	2.162
r_scbond_it	1.419
r_angle_refined_deg	1.087
r_mcangle_it	1.055
r_mcbond_it	0.663
r_symmetry_hbond_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.609
r_dihedral_angle_3_deg	14.258
r_dihedral_angle_4_deg	10.69
r_dihedral_angle_1_deg	7.811
r_scangle_it	2.162
r_scbond_it	1.419
r_angle_refined_deg	1.087
r_mcangle_it	1.055
r_mcbond_it	0.663
r_symmetry_hbond_refined	0.317
r_nbtor_refined	0.3
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2732
Nucleic Acid Atoms
Solvent Atoms	232
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 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.