6AA8 | pdb_00006aa8

Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium acetobutylicum complexed with NAD+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R1N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	17.5% PEG 3350, 200mM sodium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.375	α = 90
b = 157.939	β = 100.91
c = 81.797	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 270		2018-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.9800	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	50	98.6	0.049	0.996	14.1	2.2		109647

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14			0.316	0.829

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4R1N	2.1	48.46	104116	5496	98.33	0.19402	0.19244	0.2	0.22364	0.22	RANDOM	36.829

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]
0.19		0.38	-1.28		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.348
r_dihedral_angle_4_deg	20.808
r_dihedral_angle_3_deg	14.742
r_dihedral_angle_1_deg	5.69
r_long_range_B_other	4.826
r_long_range_B_refined	4.825
r_scangle_other	3.679
r_mcangle_it	2.759
r_mcangle_other	2.759
r_scbond_it	2.359
r_scbond_other	2.359
r_mcbond_it	1.87
r_mcbond_other	1.869
r_angle_refined_deg	1.308
r_angle_other_deg	0.759
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12749
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing