2PSW | pdb_00002psw

Human MAK3 homolog in complex with CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OB0	PDB entry 2OB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of CoA in 20 mM HEPES pH 7.5, 0.1 M NaCl, 2.5% 1,2-Propanediol, and 10 mM DTT. Cryo: 75% Reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.643	α = 90
b = 102.913	β = 105.81
c = 67.157	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 210	1-M LONG, CYLINDRICALLY BENT ULE GLASS MIRROR WITH PT AND PD COATINGS	2006-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	40.26	98.7	0.1	15.9	3.7	36244	36244		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	98.6		2.3	3.8	3597

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 2OB0	2.1	40.26	35854	34021	1833	98.61	0.2006	0.19709	0.1981	0.26463	0.2607	RANDOM	47.862

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		-0.01	-0.16		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.666
r_dihedral_angle_4_deg	17.652
r_dihedral_angle_3_deg	16.446
r_dihedral_angle_1_deg	5.775
r_scangle_it	4.756
r_scbond_it	3.462
r_mcangle_it	2.616
r_mcbond_it	1.818
r_angle_refined_deg	1.512
r_nbtor_refined	0.305
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.202
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3667
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
ARP/wARP	model building