3IKJ | pdb_00003ikj

Structural characterization for the nucleotide binding ability of subunit A mutant S238A of the A1AO ATP synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VDZ	PDB entry 1VDZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	50%(v/v) MPD, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.214	α = 90
b = 128.214	β = 90
c = 105.825	γ = 90

Symmetry
Space Group	P 43 21 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	2008-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.000	SPring-8	BL26B2

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	2.4	50	99.9	0.08	26.6	12.2	35008	33167	3	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	99.9		0.39	5.32	12.2	3428

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 1VDZ	2.4	29.84	33167	33167	1752	99.92	0.24	0.24267	0.23935	0.2507	0.30363	0.3013	RANDOM	55.732

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]
-0.02			-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.481
r_dihedral_angle_4_deg	24.29
r_dihedral_angle_3_deg	18.574
r_dihedral_angle_1_deg	6.966
r_scangle_it	4.644
r_scbond_it	2.74
r_mcangle_it	1.989
r_angle_refined_deg	1.797
r_mcbond_it	1.073
r_chiral_restr	0.119
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4055
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	32

Software

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