9JIV | pdb_00009jiv

Macrophage migration inhibitory factor Y100H mutant (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
2.7	54.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.917	α = 90
b = 68.172	β = 90
c = 87.315	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		2021-11-22	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	1.25	48.161	99.7	0.046	0.999	19.7	8.4		112191

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			0.681	0.845	3

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	48.161	112108	5670	99.676	0.127	0.1254	0.1273	0.1517	0.1532	16.159

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]
0.008			0.023		-0.031

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.276
r_lrange_it	15.97
r_lrange_other	13.123
r_dihedral_angle_3_deg	10.887
r_scangle_it	10.286
r_scangle_other	10.283
r_scbond_it	7.688
r_scbond_other	7.685
r_dihedral_angle_2_deg	6.605
r_dihedral_angle_1_deg	5.764
r_mcangle_it	4.705
r_mcangle_other	4.704
r_rigid_bond_restr	4.67
r_mcbond_it	3.673
r_mcbond_other	3.668
r_angle_refined_deg	1.858
r_angle_other_deg	0.701
r_xyhbond_nbd_refined	0.234
r_nbd_refined	0.232
r_symmetry_xyhbond_nbd_refined	0.226
r_nbd_other	0.201
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_other	0.151
r_symmetry_nbd_refined	0.151
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.081
r_chiral_restr_other	0.021
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
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	565
Heterogen Atoms	50

Software

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