4N5M

Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from Ralstonia eutropha in complexed with acetoacetyl-CoA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	ethanol, citrate, lithium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.57	α = 90
b = 139.57	β = 90
c = 70.621	γ = 90

Symmetry
Space Group	P 4 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 270		2013-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97949	PAL/PLS	7A (6B, 6C1)

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	1.34	50	99.4	0.067	56.5	16.1		151127

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	1.34	1.37	99		0.295	5.6	7.9

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	1q7b	1.34	23.39	146641	7752	99.35	0.1691	0.1681	0.1878	RANDOM	19.4431

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]
0.57			0.57		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.157
r_dihedral_angle_4_deg	20.642
r_dihedral_angle_3_deg	11.723
r_dihedral_angle_1_deg	5.748
r_mcangle_it	2.973
r_angle_refined_deg	2.446
r_mcbond_it	2.013
r_mcbond_other	2.004
r_angle_other_deg	1.048
r_chiral_restr	0.175

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.157
r_dihedral_angle_4_deg	20.642
r_dihedral_angle_3_deg	11.723
r_dihedral_angle_1_deg	5.748
r_mcangle_it	2.973
r_angle_refined_deg	2.446
r_mcbond_it	2.013
r_mcbond_other	2.004
r_angle_other_deg	1.048
r_chiral_restr	0.175
r_bond_refined_d	0.027
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3702
Nucleic Acid Atoms
Solvent Atoms	543
Heterogen Atoms	144

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
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.