9YY9 | pdb_00009yy9

Macrophage Migration Inhibitory Factor 1 from Heligmosomoides polygyrus

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A0A183FYG9-F1	Foldseek via Uniprot

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298.15	0.1 M Na Acet 4.5 pH (Buffer), 25 %w/v PEG 3350 (Precipitant)

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.654	α = 90
b = 71.654	β = 90
c = 73.125	γ = 120

Symmetry
Space Group	H 3

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		2023-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97934	NSLS-II	17-ID-2

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	1.62	28.51	97.5	0.224	0.965	9	4.7		17545

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	1.62	1.66	67.8		0.519	0.822	2.4	3.9

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	FREE R-VALUE	1.62	28.51	17545	893	97.597	0.144	0.142	0.1419	0.1747	0.1747	17.455

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]
-0.023	-0.012		-0.023		0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.524
r_lrange_it	12.364
r_lrange_other	11.983
r_dihedral_angle_3_deg	11.713
r_scangle_it	10.954
r_scangle_other	10.945
r_dihedral_angle_2_deg	9.744
r_scbond_it	7.797
r_scbond_other	7.789
r_mcangle_other	5.912
r_dihedral_angle_1_deg	5.903
r_mcangle_it	5.889
r_rigid_bond_restr	5.367
r_mcbond_it	4.329
r_mcbond_other	4.203
r_angle_refined_deg	1.819
r_angle_other_deg	0.597
r_nbd_refined	0.226
r_symmetry_nbd_other	0.194
r_nbd_other	0.18
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.119
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.084
r_symmetry_nbd_refined	0.037
r_chiral_restr_other	0.035
r_bond_refined_d	0.014
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	885
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
FAST_DP	data reduction
PHASER	phasing