2J5L

Structure of a Plasmodium falciparum apical membrane antigen 1-Fab F8. 12.19 complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J4W	PDB ENTRY 2J4W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6	290	CRYSTALLISATION TRIALS WERE CARRIED OUT WITH PFAMA1 ECTOPLASMIC CONSTRUCTION CORRESPONDING TO DOMAINS II-III. THE FAB FRAGMENT WAS INCUBATED IN SMALL STOICHIOMETRIC EXCESS WITH THE RECOMBINANT PROTEIN (1.2:1) BEFORE ADDING CRYSTALLISATION BUFFERS. CRYSTALLISATION DROPS WERE PREPARED BY MIXING 0.8 MICROL OF PROTEIN WITH 0.8 MICROL OF RESERVOIR BUFFER COMPRISING 12% PEG 6000 AND 0.1 M SODIUM ACETATE AT PH 4.6. THE FINAL PROTEIN CONCENTRATION WAS 3.2 MG/ML. CRYSTALS APPEARED AFTER 5 DAYS AT 17 DEGREE C.

Crystal Properties
Matthews coefficient	Solvent content
2.2	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.9	α = 90
b = 171.9	β = 90
c = 44.2	γ = 120

Symmetry
Space Group	P 63

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 CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.8	20	96	0.25	12.1	21.2		18102		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	3	80.4		1.16	2.7	16.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	PDB ENTRY 2J4W	2.9	20	16037	847	99.8	0.215	0.212	0.278	RANDOM	61.04

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]
-6.02	-3.01		-6.02		9.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.189
r_dihedral_angle_4_deg	25.941
r_dihedral_angle_3_deg	25.326
r_dihedral_angle_1_deg	9.908
r_scangle_it	3.714
r_mcangle_it	3.059
r_scbond_it	2.614
r_angle_refined_deg	2.386
r_mcbond_it	1.745
r_symmetry_hbond_refined	0.34
r_nbtor_refined	0.336
r_nbd_refined	0.288
r_symmetry_vdw_refined	0.25
r_xyhbond_nbd_refined	0.235
r_chiral_restr	0.146
r_bond_refined_d	0.024
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3605
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing