8REK | pdb_00008rek

Plasmodium vivax Apical Membrane Antigen 1/Fab complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W81
experimental model	PDB	6YHQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	290	Crystals were obtained by mixing 0.8 micro-L of PvAMA1-Fab complex with 0.2 micro-L of 15% 1,2,3 heptanetriol and 0.8 micro-L of reservoir buffer comprising 20% PEG 2000 monomethylether and 0.1 M Tris pH 7. The final protein concentration was 3.2 mg/ml.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.39	α = 90
b = 214.68	β = 90
c = 57.41	γ = 90

Symmetry
Space Group	P 21 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 210r		2006-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.05	73.39	99.9	0.167	0.181	0.067	0.996	11.8	7.1		18062

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.05	3.26		100	1.203	1.296	0.48	0.316		7.2

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	3.05	69.54	17069	946	99.87	0.22508	0.22134	0.2194	0.29202	0.2932	RANDOM	95.223

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]
-0.76			0.41		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.615
r_long_range_B_refined	8.205
r_long_range_B_other	8.205
r_dihedral_angle_1_deg	6.666
r_mcangle_other	5.818
r_mcangle_it	5.814
r_scangle_other	5.545
r_mcbond_it	3.616
r_mcbond_other	3.615
r_scbond_it	3.346
r_scbond_other	3.346
r_dihedral_angle_2_deg	3.302
r_angle_refined_deg	1.646
r_angle_other_deg	0.787
r_chiral_restr	0.086
r_bond_refined_d	0.021
r_bond_other_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6293
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing