Experiment: 6BPA

Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 3E9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5W53	5W53,5EN2
experimental model	PDB	5EN2	5W53,5EN2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	0.2 M KBr, 15% (w/v) PEG 4,000 and 0.05 M sodium citrate/citric acid

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.07	α = 90
b = 177.1	β = 90
c = 178.62	γ = 90

Symmetry
Space Group	P 2 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 315r		2016-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	2.53	59.54	99.8	0.993	9.9	6.7		63529

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	2.53	2.59	99.3		0.552	1.9	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5W53,5EN2	2.53	56.051	1.35	63452	1039	99.73	0.1947	0.1942	0.1958	0.2246	0.2281	44.0516

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.365
f_angle_d	0.632
f_chiral_restr	0.041
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11516
Nucleic Acid Atoms
Solvent Atoms	542
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	model building
PDB_EXTRACT	data extraction