3GK7 | pdb_00003gk7

Crystal structure of 4-hydroxybutyrate CoA-Transferase from Clostridium aminobutyricum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OAS	PDB-entry 2OAS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.0015mL protein solution (100mM Tris/HCl, pH 7.0, 150mM NaCl), 0.0003mL spermidine, 0.0012mL reservoir solution (20% PEG 550 MME, 0.1M HEPES, pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.589	α = 90
b = 116.589	β = 90
c = 174.328	γ = 90

Symmetry
Space Group	P 41 2 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	MARMOSAIC 225 mm CCD	mirrors	2008-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0707	SLS	X10SA

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	1.85	50	98.8	0.124	0.124	12	4.4	101118	99904			18.9

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)
	1.85	1.9	94.1		0.574	0.574	1.5	3	9481

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB-entry 2OAS	1.85	15	97046	95678	5028	98.59	0.18751	0.1863	0.19	0.2106	0.21	RANDOM	18.911

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]
0.46			0.46		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.553
r_dihedral_angle_4_deg	19.997
r_dihedral_angle_3_deg	13.86
r_dihedral_angle_1_deg	5.772
r_scangle_it	3.145
r_scbond_it	1.941
r_angle_refined_deg	1.211
r_mcangle_it	1.075
r_mcbond_it	0.686
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.197
r_nbd_refined	0.196
r_symmetry_hbond_refined	0.191
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6812
Nucleic Acid Atoms
Solvent Atoms	434
Heterogen Atoms	36

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling