5BS9

Crystal structure of N109A mutant of human macrophage migration inhibitory factor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	2 M ammonium sulfate, 3% 2-propanol, 0.1 M Tris-HCl, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.67	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.682	α = 90
b = 67.82	β = 90
c = 86.068	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	PIXEL	DECTRIS PILATUS 200K		2015-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	1.98	50	99.4	0.017	0.02	0.01	25.8	3.3		28104

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	1.98	2.01	99.6		0.028	0.034	0.019	0.996		2.9	1347

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	PDB entry 3DJH	1.98	47.91	26633	1432	99.35	0.1592	0.1578	0.1851	RANDOM	22.261

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]
			0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.485
r_dihedral_angle_4_deg	18.842
r_dihedral_angle_3_deg	12.83
r_dihedral_angle_1_deg	5.071
r_angle_other_deg	4.201
r_mcangle_it	2.006
r_angle_refined_deg	1.809
r_mcbond_it	1.631
r_mcbond_other	1.625
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.485
r_dihedral_angle_4_deg	18.842
r_dihedral_angle_3_deg	12.83
r_dihedral_angle_1_deg	5.071
r_angle_other_deg	4.201
r_mcangle_it	2.006
r_angle_refined_deg	1.809
r_mcbond_it	1.631
r_mcbond_other	1.625
r_chiral_restr	0.122
r_gen_planes_other	0.021
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2553
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	45

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
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 R01GM133198.