8DFH | pdb_00008dfh

Crystal structure of non-neutralizing / interfering human monoclonal antibody 42C3 Fab in complex with MSP1-19

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OB1	PDB entries 1OB1 & 6UMX
experimental model	PDB	6UMX	PDB entries 1OB1 & 6UMX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291.15	0.1 M Sodium Cacodylate, pH 6.5, 5 % (v/v) PEG 8000, 40% (v/v) 2-Methyl-2,4-Pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.39	α = 90
b = 75.72	β = 90
c = 117.53	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X 16M		2020-07-06	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.3	19.83	96.5	0.996	10.99	3.68		28468			47.38

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	93.4		0.996

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entries 1OB1 & 6UMX	2.3	19.83	1.38	28461	1424	96.72	0.2105	0.2093	0.2329	0.2656	53.32

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.8592
f_angle_d	0.5674
f_chiral_restr	0.0445
f_plane_restr	0.0029
f_bond_d	0.0022

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3928
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
PHASER	phasing