Experiment: 9B0M

Crystal structure of Macrophage migration inhibitory factor from Plasmodium vivax

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	291	Index D5: 25% w/v Polyethylene glycol 3,350, 0.1 M Sodium acetate trihydrate pH 4.5, PlviB.00834.a.UX1.PW39232 at 12 mg/mL. plate 13719 D5 drop 3. Puck: PSL-0913, Cryo: 80% crystallant + 20% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.457	α = 90
b = 75.457	β = 90
c = 36.947	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	PIXEL	DECTRIS EIGER2 XE 9M		2024-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9786	NSLS-II	19-ID

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	1.8	37.73	100	0.119	0.124	0.034	0.994	11.2	13.7		11324

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	1.8	1.84		100	1.878	1.948	0.514	0.664		14.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	37.73	1.34	11293	534	99.77	0.1883	0.1868	0.1933	0.2176	0.226

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	16.479
f_angle_d	0.944
f_chiral_restr	0.05
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	734
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	13

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing