3RF7 | pdb_00003rf7

Crystal structure of an Iron-containing alcohol dehydrogenase (Sden_2133) from Shewanella denitrificans OS-217 at 2.12 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.9	277	0.300M calcium chloride, 26.00% polyethylene glycol 400, 0.1M HEPES pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.074	α = 90
b = 121.074	β = 90
c = 275.666	γ = 90

Symmetry
Space Group	I 41 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	MARMOSAIC 325 mm CCD	FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR	2009-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.12	29.947	100	0.166	8.1	7.4	58332	58332			33.086

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	2.12	2.18	100		1.388	1.388	1.6	7.5	4226

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	SAD	THROUGHOUT	2.12	29.947	58283	2951	99.92	0.1826	0.1819	0.1927	0.1968	0.2	RANDOM	38.9231

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]
1.28			1.28		-2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.185
r_dihedral_angle_4_deg	23.458
r_dihedral_angle_3_deg	13.581
r_dihedral_angle_1_deg	5.623
r_scangle_it	3.103
r_scbond_it	2.091
r_angle_refined_deg	1.411
r_mcangle_it	1.332
r_angle_other_deg	0.909
r_mcbond_it	0.699

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.185
r_dihedral_angle_4_deg	23.458
r_dihedral_angle_3_deg	13.581
r_dihedral_angle_1_deg	5.623
r_scangle_it	3.103
r_scbond_it	2.091
r_angle_refined_deg	1.411
r_mcangle_it	1.332
r_angle_other_deg	0.909
r_mcbond_it	0.699
r_mcbond_other	0.135
r_chiral_restr	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2787
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	83

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	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.