6OYE | pdb_00006oye

Crystal structure of Y99F mutant of human macrophage migration inhibitory factor

X-RAY DIFFRACTION

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 M ammonium sulfate, 3 % 2-propanol, 0.1 M Tris-HCl, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.092	α = 90
b = 68.113	β = 90
c = 86.737	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 PILATUS 200K		2018-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.53	50	98.8	0.035	0.038	0.013	14.6	6.7		60854

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	1.53	1.56	95		0.3	0.337	0.147	0.935		4.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3DJH	1.53	48.16	57876	2905	98.76	0.147	0.1459	0.16	0.1681	0.17	RANDOM	13.461

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.462
r_dihedral_angle_4_deg	15.509
r_dihedral_angle_3_deg	10.354
r_dihedral_angle_1_deg	5.767
r_angle_other_deg	2.401
r_angle_refined_deg	1.76
r_chiral_restr	0.093
r_bond_other_d	0.035
r_bond_refined_d	0.016
r_gen_planes_other	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.462
r_dihedral_angle_4_deg	15.509
r_dihedral_angle_3_deg	10.354
r_dihedral_angle_1_deg	5.767
r_angle_other_deg	2.401
r_angle_refined_deg	1.76
r_chiral_restr	0.093
r_bond_other_d	0.035
r_bond_refined_d	0.016
r_gen_planes_other	0.014
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2574
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	55

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM157729.