7QRH

Crystal structure of the 5-(aminomethyl)furan-3-yl methyl phosphate kinase MfnE from Methanococcus vannielii.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.5, 35% w/v PAA 2100

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.147	α = 90
b = 86.147	β = 90
c = 234.105	γ = 120

Symmetry
Space Group	P 65 2 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	PIXEL	DECTRIS EIGER2 XE 16M		2020-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.36	78.04	100	1	22.3	113.8		22089

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.45			0.306

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	TrRosetta	2.36	74.717	21957	1097	99.524	0.206	0.2036	0.2576

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]
0.762	0.381		0.762		-2.472

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.634
r_dihedral_angle_4_deg	19.215
r_dihedral_angle_3_deg	15.422
r_lrange_it	12.771
r_lrange_other	12.77
r_scangle_it	10.478
r_scangle_other	10.478
r_mcangle_it	9.338
r_mcangle_other	9.336
r_scbond_it	7.751
r_scbond_other	7.705
r_dihedral_angle_1_deg	7.038
r_mcbond_other	6.993
r_mcbond_it	6.991
r_angle_other_deg	2.327
r_angle_refined_deg	1.528
r_symmetry_nbd_refined	0.243
r_nbd_other	0.229
r_symmetry_nbd_other	0.221
r_nbd_refined	0.196
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.064
r_bond_other_d	0.035
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3245
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	model building
PHASER	phasing
xia2	data scaling
xia2	data reduction