4PKZ

Crystal structure of P1M mutant of Macrophage Migration Inhibitory Factor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	2 M ammonium Sulphate, 3% 2-propanol, 20 mM Tris.HCl, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.959	α = 90
b = 95.959	β = 90
c = 104.115	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	93	IMAGE PLATE	RIGAKU RAXIS IV++		2014-03-17	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)	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	1.9	50	99.3	0.071	20.1	5.1		43923

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	99.5		0.234		5	2192

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	47.98	43810	2065	99.11	0.2263	0.2251	0.2512	RANDOM	19.267

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	41.728
r_dihedral_angle_4_deg	22.759
r_dihedral_angle_3_deg	11.374
r_dihedral_angle_1_deg	5.752
r_angle_other_deg	3.705
r_mcangle_it	2.257
r_angle_refined_deg	1.826
r_mcbond_it	1.664
r_mcbond_other	1.66
r_chiral_restr	0.114
r_bond_refined_d	0.021
r_gen_planes_other	0.021
r_gen_planes_refined	0.011
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2491
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	27

Software

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