7N09 | pdb_00007n09

Structural basis for branched substrate selectivity in a ketoreductase from Ascaris suum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E6W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	290	35% PEG550 MME, 144 mM potassium sodium tartrate, 100 mM MES, pH6.5 2 M sodium malonate, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.542	α = 90
b = 54.942	β = 131.039
c = 89.27	γ = 90

Symmetry
Space Group	C 1 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 PILATUS3 S 6M		2017-05-05	L	MAD
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.73	ALS	8.3.1
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	2.5	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	67.33	89.4	0.999	12.5	2		84379			31.22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81			0.196

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1e6w	2	67.33	1.33	62168	2821	99.77	0.1789	0.177	0.18	0.22	0.22	35.99

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	15.4025
f_angle_d	1.1045
f_chiral_restr	0.57
f_bond_d	0.0159
f_plane_restr	0.0077

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3798
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	88

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
BALBES	phasing
Coot	model building

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.