2Q8A | pdb_00002q8a

Structure of the malaria antigen AMA1 in complex with a growth-inhibitory antibody

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z40	1Z40, 2CGR
experimental model	PDB	2CGR	1Z40, 2CGR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	294	20 MM MES, 10 MM MNCL2, 6 % PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 189.762	α = 90
b = 51.203	β = 111.09
c = 91.518	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	RIGAKU RAXIS IV++	osmic multilayer		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.4	40	99.9	0.061	13	4	30851	30851		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	99.9		0.23	4.7	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1Z40, 2CGR	2.4	38.92	32498	32498	1647	100	0.20433	0.20433	0.20215	0.2	0.2445	0.24	RANDOM	35.073

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]
-2.33		-1.66	1.26		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.66
r_dihedral_angle_4_deg	20.436
r_dihedral_angle_3_deg	15.265
r_dihedral_angle_1_deg	6.096
r_scangle_it	1.483
r_angle_refined_deg	1.138
r_scbond_it	0.896
r_mcangle_it	0.57
r_mcbond_it	0.315
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.66
r_dihedral_angle_4_deg	20.436
r_dihedral_angle_3_deg	15.265
r_dihedral_angle_1_deg	6.096
r_scangle_it	1.483
r_angle_refined_deg	1.138
r_scbond_it	0.896
r_mcangle_it	0.57
r_mcbond_it	0.315
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.186
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.18
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5544
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.