2XCZ

Crystal Structure of macrophage migration inhibitory factor homologue from Prochlorococcus marinus

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GIF	PDB ENTRIES 1GIF, 1GCZ, 1FIM, 1UIZ.
experimental model	PDB	1GCZ	PDB ENTRIES 1GIF, 1GCZ, 1FIM, 1UIZ.
experimental model	PDB	1FIM	PDB ENTRIES 1GIF, 1GCZ, 1FIM, 1UIZ.
experimental model	PDB	1UIZ	PDB ENTRIES 1GIF, 1GCZ, 1FIM, 1UIZ.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	42% PEG300, 0.2 M SODIUM CHLORIDE, 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP,TEMPERATURE 298 K

Crystal Properties
Matthews coefficient	Solvent content
1.94	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.45	α = 90
b = 52.45	β = 90
c = 63.99	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MACSCIENCE DIP2030H	MIRRORS	2009-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591

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	1.63	26.2	98.7	0.07	15.3	5.6		12309		-3	15.1

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	1.63	1.72	91.3		0.26	6.4	4.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1GIF, 1GCZ, 1FIM, 1UIZ.	1.64	26.22	11702	590	99.69	0.16604	0.16377	0.21277	RANDOM	16.213

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	40.747
r_dihedral_angle_3_deg	12.321
r_dihedral_angle_4_deg	7.735
r_dihedral_angle_1_deg	5.524
r_scangle_it	3.607
r_scbond_it	2.086
r_angle_refined_deg	1.157
r_mcangle_it	1.149
r_mcbond_it	0.563
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	858
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing