2FHK

Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FTR	PDB ID 1FTR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	12-18 % PEG 8000, 20 % glycerol, 0.5 M KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86	α = 90
b = 74.2	β = 113.6
c = 103.6	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	281	CCD	ADSC QUANTUM 4		2004-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.91	ESRF	ID14-4

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	2	104	98.1	0.156	7.64			80885

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)
	2	2.1	96.6		0.443	3.91		10589

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 1FTR	2	20	80587	80587	4030	99.75	0.219	0.219	0.218	0.245	RANDOM	19.398

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]
2.64		1.07	-0.8		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.6
r_dihedral_angle_3_deg	13.171
r_dihedral_angle_4_deg	11.879
r_scangle_it	6.502
r_dihedral_angle_1_deg	5.347
r_scbond_it	4.016
r_mcangle_it	2.175
r_angle_refined_deg	1.152
r_mcbond_it	1.087
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.284
r_symmetry_hbond_refined	0.226
r_nbd_refined	0.216
r_xyhbond_nbd_refined	0.139
r_metal_ion_refined	0.112
r_symmetry_metal_ion_refined	0.081
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8897
Nucleic Acid Atoms
Solvent Atoms	474
Heterogen Atoms	113

Software

Software
Software Name	Purpose
DENZO	data reduction
XSCALE	data scaling
EPMR	phasing
REFMAC	refinement