3P20 | pdb_00003p20

Crystal structure of vanadate bound subunit A 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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	50% (v/v) MPD, 2mM sodium orthovanadate, 2mM Magnesium chloride and 0.1M acetate (pH 4.5), vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.55	α = 90
b = 127.55	β = 90
c = 104.064	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	ADSC QUANTUM 4r	mirrors	2010-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	1.00	SPring-8	BL12B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.85	30	100	0.087	7.3	8.8	20571	20534			69.93

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.86	2.96	100		0.458		8.2	2010

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	1vdz	2.85	29.25	20534	20488	1042	99.99	0.2116	0.2097	0.2062	0.2457	0.2182	RANDOM	50.3054

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.786
r_dihedral_angle_4_deg	23.738
r_dihedral_angle_3_deg	20.983
r_dihedral_angle_1_deg	8.711
r_scangle_it	4.158
r_scbond_it	2.308
r_angle_refined_deg	1.789
r_mcangle_it	1.514
r_mcbond_it	0.78
r_chiral_restr	0.118
r_bond_refined_d	0.015
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4086
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	66

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling