3QDQ | pdb_00003qdq

Complex between 4-hydroxybutyrate CoA-transferase from Clostridium aminobutyricum and CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GK7	PDB ENTRY 3GK7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	CRYSTALLIZATION CONDITIONS: 0.1 M SPERMIDINE, 20% PEG 550 MME, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.215	α = 90
b = 118.215	β = 90
c = 87.392	γ = 90

Symmetry
Space Group	P 42 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	2009-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00	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	2.6	50	96.8	0.128	0.128	14.7	4.3	19019	18410			50.8

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	2.6	2.69	94.5		0.601	0.601	3.2	3.7	1818

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 (All)	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 3GK7	2.6	50	18640	18006	959	96.6	0.221	0.22091	0.21809	0.2151	0.27354	0.2655	RANDOM	38.016

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]
2.49			2.49		-4.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.715
r_dihedral_angle_3_deg	19.84
r_dihedral_angle_4_deg	14.636
r_dihedral_angle_1_deg	7.057
r_scangle_it	2.775
r_scbond_it	1.865
r_angle_refined_deg	1.68
r_mcangle_it	1.164
r_mcbond_it	0.681
r_nbtor_refined	0.317
r_symmetry_vdw_refined	0.253
r_nbd_refined	0.247
r_xyhbond_nbd_refined	0.187
r_symmetry_hbond_refined	0.167
r_chiral_restr	0.118
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3414
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	48

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling