2GVI

Crystal structure of a putative formylmethanofuran dehydrogenase subunit e (ta1109) from thermoplasma acidophilum at 1.87 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6	277	10.0% PEG-8000, 0.2M Zn(OAc)2, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP	6	277	0.2M MgNO3, 20.0% PEG-3350, No Buffer pH 5.8, pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.68	α = 90
b = 97.65	β = 90
c = 75.27	γ = 90

Symmetry
Space Group	I 2 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	CCD	ADSC QUANTUM 315	Flat mirror (vertical focusing)	2006-03-19	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2006-03-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	1.000001	SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97918, 0.91837, 0.97903	SSRL	BL9-2

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	1.87	30.08	99.5	0.114	8.38	4.05		24246			28.07

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)
1,2	1.87	1.94	99.5	99.5	0.698	1.27

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD, MOLECULAR REPLACEMENT	THROUGHOUT	1.87	30.08	24246	1229	99.66	0.191	0.19109	0.19	0.217	RANDOM	31.123

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]
0.56			0.9		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.197
r_dihedral_angle_3_deg	10.225
r_dihedral_angle_4_deg	9.874
r_scangle_it	5.003
r_scbond_it	3.861
r_dihedral_angle_1_deg	3.609
r_mcangle_it	2.323
r_angle_refined_deg	1.644
r_mcbond_it	1.53
r_angle_other_deg	1.131
r_mcbond_other	0.328
r_symmetry_hbond_refined	0.22
r_nbd_refined	0.179
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.153
r_metal_ion_refined	0.144
r_symmetry_vdw_other	0.141
r_symmetry_vdw_refined	0.14
r_nbd_other	0.125
r_chiral_restr	0.097
r_symmetry_metal_ion_refined	0.09
r_nbtor_other	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1582
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing
PHASER	phasing