9JIZ | pdb_00009jiz

Macrophage migration inhibitory factor S61H/Y100H mutant complexed with three Zinc ions (Zn3-MIF(S61H/Y100H))

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DJH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	2.0M ammonium sulfate, 20mM Tris-HCl buffer (pH 7.5), 3% isopropanol

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.35	α = 90
b = 68.609	β = 90
c = 86.785	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	100	PIXEL	DECTRIS EIGER X 16M		2024-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.3	48.42	100	0.097	0.995	10.8	6.8		100854

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32			0.923	0.729	2.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.3	48.42	100771	5096	99.996	0.138	0.1369	0.1426	0.1673	0.1731	14.52

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]
-0.042			0.052		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.059
r_dihedral_angle_6_deg	16.69
r_lrange_other	15.175
r_dihedral_angle_3_deg	10.274
r_scangle_it	9.143
r_scangle_other	9.141
r_dihedral_angle_2_deg	7.222
r_scbond_it	6.91
r_scbond_other	6.908
r_dihedral_angle_1_deg	5.842
r_mcangle_other	4.419
r_mcangle_it	4.418
r_rigid_bond_restr	4.414
r_mcbond_it	3.396
r_mcbond_other	3.392
r_angle_refined_deg	1.825
r_angle_other_deg	0.673
r_symmetry_xyhbond_nbd_other	0.421
r_symmetry_xyhbond_nbd_refined	0.389
r_symmetry_nbd_refined	0.278
r_xyhbond_nbd_refined	0.248
r_nbd_refined	0.24
r_nbd_other	0.235
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.174
r_chiral_restr	0.107
r_metal_ion_refined	0.084
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2607
Nucleic Acid Atoms
Solvent Atoms	510
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing