5HVT

Crystal Structure of Macrophage Migration Inhibitory Factor (MIF) with a Potent Inhibitor (NVS-2)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	2.0 M Ammonium Sulfate, 3% isopropanol and 0.1 M Tris pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.74	67.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.023	α = 90
b = 96.023	β = 90
c = 104.039	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	100	CCD	RIGAKU SATURN 944+		2015-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (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
1	1.75	83.16	100	0.086	0.092	0.032	15.3	7.1		56173

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	1.75	1.78	99.9		0.795	0.919	0.457	0.646		4	2741

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2OOH	1.75	83.16	50398	5644	99.72	0.1798	0.1773	0.2027	RANDOM	20.916

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]
-0.07	-0.03		-0.07		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.458
r_dihedral_angle_4_deg	17.459
r_dihedral_angle_3_deg	12.055
r_dihedral_angle_1_deg	5.636
r_mcangle_it	1.514
r_angle_refined_deg	1.407
r_mcbond_it	1.043
r_mcbond_other	1.041
r_angle_other_deg	0.954
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.458
r_dihedral_angle_4_deg	17.459
r_dihedral_angle_3_deg	12.055
r_dihedral_angle_1_deg	5.636
r_mcangle_it	1.514
r_angle_refined_deg	1.407
r_mcbond_it	1.043
r_mcbond_other	1.041
r_angle_other_deg	0.954
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2589
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

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.