6HUX

HmdII from Methanocaldococcus jannaschii reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydromethanopterin at 2.5 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YT4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	281	HmdII from Methanocaldococcus jannaschii reconstituted with Fe-guanylylpyridinol cofactor was cocrystallized with methenyl-tetrahydromethanopterin using the sitting drop vapor diffusion method under N2/H2 (95%/5%) in red light condition. 20 mg/ml of reconstituted enzyme in 25 mM Tris pH 7.5, 5% glycerol, 150 mM NaCl, 2 mM DTT and 3 mM methenyl-tetrahydromethanopterin was spotted on a 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK) with a ratio of 0.7 ul of protein and 0.7 ul of reservoir solution. After several weeks, crystals appeared in 2 M LiSO4, 100 mM Sodium acetate pH 5.5, 100 mM MgSO4 and 5% v/v PEG 400. jHmdII crystal was cryoprotected in its mother liquor supplemented with 30% ethylene glycol before freezing in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.281	α = 90
b = 124.281	β = 90
c = 150.086	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2017-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.9799	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.5	43.73	100	0.122	0.129	0.041	0.997	13.1	9.8		15610			64.85

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	2.5	2.64	99.9		1.341	1.415	0.447	0.686	2.2	9.9

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	4YT4	2.5	38.97	15602	739	99.9	0.168	0.165	0.219	RANDOM	64.84

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]
2.8028			2.8028		-5.6056

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.91
t_omega_torsion	2.07
t_angle_deg	0.99
t_bond_d	0.008
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.91
t_omega_torsion	2.07
t_angle_deg	0.99
t_bond_d	0.008
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2790
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	157

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

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.