4K6F

X-ray crystal structure of a putative Acetoacetyl-CoA reductase from Burkholderia cenocepacia bound to the co-factor NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4K6C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	JCSG+ G4: 0.1 M TRIS-HCl, 200 mM trimethylamine N-oxide, 20% PEG 2000 MME , pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.74	α = 90
b = 101.33	β = 90
c = 134.56	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD		2013-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.5	47.415	99.1	0.063	19.78		146320	145003		-3	19.215

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	1.5	1.54	98.4		0.546	3.71

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	4K6C	1.5	47.46	146320	137740	7264	99.13	0.1676	0.1652	0.2126	RANDOM	15.131

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]
-0.12			-0.38		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.024
r_sphericity_free	32.668
r_dihedral_angle_4_deg	11.216
r_dihedral_angle_3_deg	10.982
r_sphericity_bonded	7.913
r_dihedral_angle_1_deg	5.627
r_rigid_bond_restr	2.062
r_mcangle_it	1.859
r_mcbond_it	1.572
r_mcbond_other	1.572

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.024
r_sphericity_free	32.668
r_dihedral_angle_4_deg	11.216
r_dihedral_angle_3_deg	10.982
r_sphericity_bonded	7.913
r_dihedral_angle_1_deg	5.627
r_rigid_bond_restr	2.062
r_mcangle_it	1.859
r_mcbond_it	1.572
r_mcbond_other	1.572
r_angle_refined_deg	1.409
r_angle_other_deg	0.811
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7152
Nucleic Acid Atoms
Solvent Atoms	945
Heterogen Atoms	118

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.