7XVX

Neutron crystal structure of human macrophage migration inhibitory factor

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7XTX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		283	0.49 M Monosodium phosphate, 0.91 M Dipotassium phosphate

Crystal Properties
Matthews coefficient	Solvent content
3.83	67.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.534	α = 90
b = 96.534	β = 90
c = 105.596	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	293	DIFFRACTOMETER	iBIX	The used detector is described in the paper (https://iopscience.iop.org/article/10.1088/1742-6596/528/1/012042/pdf).	2020-06-24	L	LAUE
2	1	x-ray	293	PIXEL	DECTRIS PILATUS3 6M		2020-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	3.05-5.47	JPARC MLF	BL-03
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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
2	1.6	48.27	99.9					0.996		14.7	10		75394			20.95
1	2	20	99.4					0.984		7.9	6.6		38853

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
2	1.6	1.63						0.923
1	2	2.11						0.431

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.6	44.64		1.93		75322	3993	100		0.1547	0.1539	0.1692		29.16
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2	20				38853		99.4			0.18	0.2

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.1828
f_angle_d	1.5558
f_chiral_restr	0.113
f_bond_d	0.041
f_plane_restr	0.0074

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2579
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

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 R01GM133198.