3D00 | pdb_00003d00

Crystal structure of a tungsten formylmethanofuran dehydrogenase subunit e (fmde)-like protein (syn_00638) from syntrophus aciditrophicus at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.01M NiCl2, 20.0% PEG MME 2000, 0.1M Tris-HCl pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.356	α = 90
b = 54.356	β = 90
c = 136.719	γ = 90

Symmetry
Space Group	P 41 21 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-04-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97817	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	29.386	99.9	0.078	0.078	6.8	7		16955			30.675

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	99.9		0.011	1.134	0.7	7.1	1208

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.9	29.386	16902	855	99.9	0.235	0.233	0.24	0.268	0.27	RANDOM	35.2

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]
1.73			1.73		-3.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.474
r_dihedral_angle_4_deg	21.608
r_dihedral_angle_3_deg	14.661
r_dihedral_angle_1_deg	6.4
r_mcangle_it	1.913
r_angle_refined_deg	1.604
r_scangle_it	1.576
r_mcbond_it	1.214
r_scbond_it	1.086
r_angle_other_deg	1.031
r_mcbond_other	0.264
r_symmetry_vdw_other	0.226
r_nbd_refined	0.2
r_nbd_other	0.196
r_nbtor_refined	0.182
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.175
r_symmetry_vdw_refined	0.114
r_chiral_restr	0.088
r_nbtor_other	0.087
r_bond_refined_d	0.019
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1388
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing