1E3W | pdb_00001e3w

Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH and 3-keto butyrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HSD	PDB ENTRY 2HSD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	HANGING DROP PROT: 10MG/ML, 0.4 MM ACETOACETYL COA, 1 MM NADH, 10 MM HEP WELL: 28% PEG 4000, 0.2 M LI SO4, 0.1 M TRIS PH 8.5. 18 C

Crystal Properties
Matthews coefficient	Solvent content
2.25	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.603	α = 65.22
b = 67.426	β = 73.27
c = 67.5	γ = 75.67

Symmetry
Space Group	P 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	CCD	MARRESEARCH	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.4	40	92	0.06	0.06	19.7	2.6		148442			14.1

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	1.4	1.42	60.4		0.291	0.291	2.1

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-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2HSD	2	40	62009	3014	94.9	0.189	0.226	RANDOM	18.4

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
p_angle_d	0.03
p_bond_d	0.011
p_angle_deg
p_planar_d
p_hb_or_metal_coord
p_mcbond_it
p_mcangle_it
p_scbond_it
p_scangle_it
p_plane_restr
p_chiral_restr
p_singtor_nbd
p_multtor_nbd
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7342
Nucleic Acid Atoms
Solvent Atoms	889
Heterogen Atoms	232

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing