9EVO | pdb_00009evo

Plasmodium falciparum apical membrane antigen 3D7

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z40

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		290	Crystals of PfAMA1-3D7 were obtained by mixing 1.2 micro-L of protein and 1.2 micro-L of reservoir buffer containing 12% PEG 3350, 0.1M Hepes pH 7 and 10% propanol-2. The final protein concentration was 3.5 mg/ml. Before mounting, 1 micro-L of a 20mM solution of a small molecule NCGC00015280 (demonstrated as inhibiting the AMA1-RON2 interaction and referenced as B43 in the PDB), was dissolved in DMSO and half diluted with the reservoir buffer, then added to the drop containing the crystals. Cryo-protecting buffer for the PfAMA1-3D7 crystals consisted of 90% of reservoir buffer containing 20% PEG 3350, 0.1M Hepes pH 7 and 10% propanol-2 supplemented with 10% glycerol, and 10% of a 20mM solution of B43.

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.23	α = 89.13
b = 62.06	β = 89.9
c = 71.5	γ = 83.92

Symmetry
Space Group	P 1

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 PILATUS 6M		2014-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97857	SOLEIL	PROXIMA 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	2.1	47.06	97.9	0.199	0.268	0.179	0.902	4.3	2		37352

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	2.1	2.21			0.872	1.183	0.795	0.215	2.1

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	2.1	46.37	35400	1908	97.77	0.20977	0.20732	0.2157	0.25599	0.2675	RANDOM	26.81

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]
-0.44	-0.47	0.23	1.48	-1.01	-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.346
r_dihedral_angle_2_deg	7.741
r_dihedral_angle_1_deg	7.041
r_long_range_B_refined	6.037
r_long_range_B_other	5.992
r_scangle_other	4.054
r_mcangle_it	3.719
r_mcangle_other	3.718
r_scbond_it	2.439
r_scbond_other	2.439
r_mcbond_it	2.305
r_mcbond_other	2.304
r_angle_refined_deg	1.729
r_angle_other_deg	0.727
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.005
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	4778
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms

Software

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