3EIU

A second transient position of ATP on its trail to the nucleotide-binding site of subunit B of the motor protein A1Ao ATP synthase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C61	PDB ENTRY 2C61

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	15% glycerol, 20% PEG 400, 2mM Mg2+ ATP, 0.1M Sodium Chloride, 0.1M Sodium citrate (pH 5.0), vapor diffusion,sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.693	α = 90
b = 96.867	β = 90
c = 129.631	γ = 90

Symmetry
Space Group	P 21 21 21

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 315	mirrors	2007-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.00	NSRRC	BL13B1

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	3.4	30	91	0.167	8.493	3.5	13292	12055			78.55

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	3.4	3.52	85.7		0.473	1.94	2.4	1094

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2C61	3.43	24.62	11433	12032	595	90.52	0.308	0.249	0.246	0.315	RANDOM	72.12

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]
0.18			-0.01		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.391
r_dihedral_angle_3_deg	20.034
r_dihedral_angle_4_deg	13.04
r_dihedral_angle_1_deg	5.199
r_angle_refined_deg	0.997
r_mcangle_it	0.421
r_scangle_it	0.417
r_nbtor_refined	0.299
r_scbond_it	0.244
r_mcbond_it	0.233

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.391
r_dihedral_angle_3_deg	20.034
r_dihedral_angle_4_deg	13.04
r_dihedral_angle_1_deg	5.199
r_angle_refined_deg	0.997
r_mcangle_it	0.421
r_scangle_it	0.417
r_nbtor_refined	0.299
r_scbond_it	0.244
r_mcbond_it	0.233
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.097
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6506
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	44

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.