3SVT

Structure of a short-chain type dehydrogenase/reductase from Mycobacterium ulcerans

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	40% PEG300, 0.1 M cacodylate, pH 6.5, 200 mM calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2	38.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.185	α = 90
b = 64.542	β = 90
c = 118.804	γ = 90

Symmetry
Space Group	P 21 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	ADSC QUANTUM 210		2011-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97	ALS	5.0.1

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	42.62	98.8	0.086	9.5	4.4		32329

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	2.03	99.8		0.406		4.5	1625

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1FMC	2	42.62	32144	1624	98.02	0.1831	0.1811	0.2193	RANDOM	30.4182

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]
3.32			-2.35		-0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.998
r_dihedral_angle_4_deg	15.243
r_dihedral_angle_3_deg	12.594
r_dihedral_angle_1_deg	6.243
r_scangle_it	3.026
r_scbond_it	1.975
r_angle_refined_deg	1.333
r_mcangle_it	1.128
r_angle_other_deg	1.066
r_mcbond_it	0.643

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.998
r_dihedral_angle_4_deg	15.243
r_dihedral_angle_3_deg	12.594
r_dihedral_angle_1_deg	6.243
r_scangle_it	3.026
r_scbond_it	1.975
r_angle_refined_deg	1.333
r_mcangle_it	1.128
r_angle_other_deg	1.066
r_mcbond_it	0.643
r_mcbond_other	0.145
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3939
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

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 R01GM133198.