3K6M | pdb_00003k6m

Dynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase from pig heart.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O9L	PDB ENTRY 1O9L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	4 ul Well Solution: 18-22% PEG 3350 or 4000, 75 mM Tris/HCl pH 8. 4 ul Protein solution: 10-15 mg/ml protein, 20 mM MOPS pH 7.2, 1 mM EDTA, 1 mM DTT, 0.2 mM PMSF, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.715	α = 90
b = 133.566	β = 104.98
c = 102.23	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	MAR CCD 130 mm		1998-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.948	ESRF	ID14-3

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	1.5	20	97.7	0.042	0.042	12	3.3	297163	297163			17.16

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	1.5	1.54	82		0.296	0.296	2.3	2.2	18372

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 1O9L	1.5	20	296782	296782	14899	97.6	0.1657	0.1657	0.16502	0.17	0.18538	0.19	RANDOM	19.924

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]
0.92		0.15	-0.76		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.68
r_dihedral_angle_4_deg	13.902
r_dihedral_angle_3_deg	12.414
r_dihedral_angle_1_deg	6.206
r_angle_other_deg	4.206
r_scangle_it	3.231
r_scbond_it	2.315
r_angle_refined_deg	1.528
r_mcangle_it	1.208
r_mcbond_it	1.114
r_symmetry_vdw_other	0.304
r_nbd_other	0.242
r_mcbond_other	0.23
r_nbd_refined	0.22
r_nbtor_refined	0.177
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.17
r_symmetry_hbond_refined	0.152
r_nbtor_other	0.111
r_chiral_restr	0.097
r_bond_refined_d	0.016
r_gen_planes_other	0.009
r_gen_planes_refined	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14137
Nucleic Acid Atoms
Solvent Atoms	1581
Heterogen Atoms	14

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling