6BG7 | pdb_00006bg7

Crystal structure of G107A 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
3.71	66.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.863	α = 90
b = 95.863	β = 90
c = 103.712	γ = 120

Symmetry
Space Group	P 31 2 1

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		2017-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	2.54	50	83.7	0.082	0.099	0.054	8.2	2.6		15576

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	2.55	2.59	83		0.384	0.476	0.274	0.812		2.4

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	2.54	47.93	14698	758	83.01	0.1998	0.1984	0.21	0.2254	0.23	RANDOM	35.66

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]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.547
r_dihedral_angle_4_deg	25.502
r_dihedral_angle_3_deg	12.459
r_dihedral_angle_1_deg	6.225
r_angle_refined_deg	1.684
r_angle_other_deg	1.072
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.547
r_dihedral_angle_4_deg	25.502
r_dihedral_angle_3_deg	12.459
r_dihedral_angle_1_deg	6.225
r_angle_refined_deg	1.684
r_angle_other_deg	1.072
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2548
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	44

Software

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

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.