1Z3G | pdb_00001z3g

Crystal structure of complex between Pvs25 and Fab fragment of malaria transmission blocking antibody 2A8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	12E8	Pvs25 model, 2E8 Fab model
experimental model	PDB	1Z1Y	Pvs25 model, 2E8 Fab model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	295	PEG6000, Lithium Chloride, Citic acid buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.78	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.262	α = 90
b = 61.649	β = 101.68
c = 142.65	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 4		2003-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97942	APS	22-ID

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	3.3	49.16	95.1	0.275	5.2	4.5	21703	21703		-3	34.2

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	3.3	3.36	87.5	87.5	0.01	1.3	4.1	21703

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	Pvs25 model, 2E8 Fab model	3.3	49.15	21703	20602	1095	94.85	0.275	0.275	0.272	0.26	0.327	0.31	RANDOM	2

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]
1.49		-4.09	-5.31		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.915
r_dihedral_angle_4_deg	25.482
r_dihedral_angle_3_deg	23.446
r_dihedral_angle_1_deg	5.987
r_angle_refined_deg	1.775
r_symmetry_vdw_refined	0.335
r_nbtor_refined	0.313
r_nbd_refined	0.274
r_symmetry_hbond_refined	0.221
r_xyhbond_nbd_refined	0.199

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.915
r_dihedral_angle_4_deg	25.482
r_dihedral_angle_3_deg	23.446
r_dihedral_angle_1_deg	5.987
r_angle_refined_deg	1.775
r_symmetry_vdw_refined	0.335
r_nbtor_refined	0.313
r_nbd_refined	0.274
r_symmetry_hbond_refined	0.221
r_xyhbond_nbd_refined	0.199
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9120
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
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.