2CYD | pdb_00002cyd

Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	296	PEG 400, Lithium chroride, Potassium citrate, Tris-HCl, Glycerol, Undecyl-maltoside, Dodecyl-maltoside, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
4.9	74.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.648	α = 90
b = 125.779	β = 90
c = 210.196	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	IMAGE PLATE	RIGAKU		2005-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0000	SPring-8	BL26B1

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	2.8	107.83		0.094	0.094	11.2	4.1	78734	77244			56

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	2.8	2.95			0.706	0.706	1.9	3.6	10723

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	2.8	107.8	1.9	77318	73353	3890	98.11	0.20861	0.20811	0.21	0.21813	0.22	RANDOM	55.981

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]
-4			2.38		1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.354
r_dihedral_angle_3_deg	14.449
r_dihedral_angle_1_deg	4.201
r_scangle_it	2.295
r_scbond_it	1.243
r_angle_refined_deg	1.134
r_mcangle_it	0.947
r_mcbond_it	0.539
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.213

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.354
r_dihedral_angle_3_deg	14.449
r_dihedral_angle_1_deg	4.201
r_scangle_it	2.295
r_scbond_it	1.243
r_angle_refined_deg	1.134
r_mcangle_it	0.947
r_mcbond_it	0.539
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.213
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.101
r_chiral_restr	0.081
r_metal_ion_refined	0.021
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11280
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	968

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

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.