9JJ0 | pdb_00009jj0

Macrophage migration inhibitory factor Y100H mutant complexed with three Zinc ions (Zn3-MIF(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
2.72	54.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.906	α = 90
b = 68.32	β = 90
c = 87.629	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 EIGER2 XE 16M		2022-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

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	1.25	48.16	100	0.046	1	23.6	13.8		113184

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	1.25	1.27			1.017	0.842	2.7

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	1.25	48.16	113094	5571	99.995	0.119	0.1177	0.1227	0.1463	0.151	18.42

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]
0.171			-0.139		-0.031

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.907
r_dihedral_angle_6_deg	17.042
r_lrange_other	15.758
r_dihedral_angle_3_deg	11.862
r_scangle_it	11.004
r_scangle_other	11.001
r_dihedral_angle_2_deg	9.261
r_scbond_it	8.224
r_scbond_other	8.221
r_dihedral_angle_1_deg	5.671
r_mcangle_it	5.583
r_mcangle_other	5.583
r_mcbond_it	4.26
r_mcbond_other	4.258
r_rigid_bond_restr	4.206
r_angle_refined_deg	1.806
r_angle_other_deg	0.664
r_xyhbond_nbd_refined	0.285
r_nbd_refined	0.244
r_nbd_other	0.237
r_symmetry_xyhbond_nbd_refined	0.217
r_symmetry_nbd_other	0.195
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.136
r_chiral_restr	0.108
r_metal_ion_refined	0.101
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_chiral_restr_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2595
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms	55

Software

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