4PKK

Crystal structure of Macrophage Migration inhibitory factor in complex with furan-2-ylmethyl)imino methanethiol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	2 M ammonium Sulphate, 3% 2-propanol, 20 mM Tris.HCl, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.702	α = 90
b = 95.702	β = 90
c = 103.662	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	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++		2013-09-11	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.78	50	100	0.027	23.7	8		52989

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81	100		0.129		7.7	2625

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.78	47.85	52953	2693	99.95	0.1626	0.1616	0.1813	RANDOM	17.949

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.542
r_dihedral_angle_4_deg	21.914
r_dihedral_angle_3_deg	9.776
r_dihedral_angle_1_deg	5.786
r_angle_other_deg	3.697
r_mcangle_it	1.974
r_angle_refined_deg	1.86
r_mcbond_it	1.523
r_mcbond_other	1.511
r_chiral_restr	0.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.542
r_dihedral_angle_4_deg	21.914
r_dihedral_angle_3_deg	9.776
r_dihedral_angle_1_deg	5.786
r_angle_other_deg	3.697
r_mcangle_it	1.974
r_angle_refined_deg	1.86
r_mcbond_it	1.523
r_mcbond_other	1.511
r_chiral_restr	0.127
r_gen_planes_other	0.023
r_bond_refined_d	0.022
r_gen_planes_refined	0.01
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2531
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	82

Software

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

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.