9EZE | pdb_00009eze

Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to human antibody DB9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6R2S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M ammonium acetate, 0.1M sodium acetate pH 4.0, 15% PEG 4000

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.427	α = 90
b = 126.191	β = 90
c = 129.863	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	PIXEL	DECTRIS EIGER2 XE 16M		2017-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9999	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.55	90.5	98.3	0.999	14.77	6.5		180370

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.605			0.58

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	1.55	90.5	178875	8857	98.3	0.2053	0.2044	0.1992	0.2232	0.1946	RANDOM	30.97

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]
2.7153			-2.0408		-0.6745

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	14.9
t_omega_torsion	4.34
t_angle_deg	1.12
t_bond_d	0.011
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8524
Nucleic Acid Atoms
Solvent Atoms	978
Heterogen Atoms

Software

Software
Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	phasing