5T5M | pdb_00005t5m

TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, TRIGONAL FORM AT 2.5 A.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5T5I	PDB : 5T5I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	100 mM Tricine/NaOH, pH 8.0, 30% (v/v) pentaerythritol propoxylate 426 (5/4 PO/OH), and 400 mM KCl. The crystallized sample has to be perfectly anoxic and extremely fresh (crystallization after 3 days of purification) without any freezing step. The optimal protein concentration is 30 mg/ml. Drops are made by mixing 1 ul of protein and 1 ul of precipitant. Crystals appeared usually after 7-10 days anoxically.

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.543	α = 90
b = 105.543	β = 90
c = 340.549	γ = 120

Symmetry
Space Group	P 32 2 1

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 PILATUS 6M-F		2015-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00005	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	2.5	48.65	100	0.09	0.035	0.998	13.6	7.5		77304

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	100		0.94	0.799	2.2	7.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB : 5T5I	2.5	48.218	1.33	77174	3638	99.91	0.1587	0.1576	0.16	0.1817	0.19	Random selection

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.598
f_angle_d	1.671
f_chiral_restr	0.135
f_bond_d	0.011
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13936
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	208

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	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.