4P01

Crystal Structure Analysis of Macrophage Migration Inhibitory Factor in complex with N-[(4-cyanophenyl)methyl]methanethioamide

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
2.76	55.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.144	α = 90
b = 68.386	β = 90
c = 87.685	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	93	IMAGE PLATE	RIGAKU RAXIS IV++		2013-10-08	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	2.07	50	99.6	0.065	10.9	4.4		25650

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.07	25.07	25499	1303	99.22	0.1877	0.1856	0.2275	RANDOM	25.562

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			-0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.84
r_dihedral_angle_4_deg	21.577
r_dihedral_angle_3_deg	11.871
r_dihedral_angle_1_deg	6.074
r_mcangle_it	3.085
r_mcbond_it	2.252
r_mcbond_other	2.244
r_angle_refined_deg	1.796
r_angle_other_deg	1.756
r_chiral_restr	0.167

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.84
r_dihedral_angle_4_deg	21.577
r_dihedral_angle_3_deg	11.871
r_dihedral_angle_1_deg	6.074
r_mcangle_it	3.085
r_mcbond_it	2.252
r_mcbond_other	2.244
r_angle_refined_deg	1.796
r_angle_other_deg	1.756
r_chiral_restr	0.167
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2502
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	41

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data reduction
Crystal	data reduction
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.