2AGV | pdb_00002agv

Crystal structure of the SR CA2+-ATPASE with BHQ and TG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IWO	3 CYTOPLASMIC DOMAINS OF CA2+-ATPASE IN 1IWO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	6.1	283	PEG400, pH 6.10, MICRODIALYSIS, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
3.468	65.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.385	α = 90
b = 71.385	β = 90
c = 591.017	γ = 90

Symmetry
Space Group	P 41

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 RAXIS V		2004-06-14	M	SINGLE WAVELENGTH
2	1		CCD	ADSC Q-315		2004-11-08

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.75	SPring-8	BL41XU

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	2.4	20	99.8	0.075	29.3	10.6	114354	114125		-3	37.9

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	2.4	2.5	99.4		0.271	4.5	5.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3 CYTOPLASMIC DOMAINS OF CA2+-ATPASE IN 1IWO	2.4	14.98	2	114041	113813	5738	99.8	0.24	0.239	0.239	0.263	RANDOM	55.9

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]
1.89			1.89		-3.77

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.8
c_scangle_it	3.73
c_mcangle_it	3.15
c_scbond_it	2.58
c_mcbond_it	1.96
c_angle_deg	1.3
c_improper_angle_d	0.85
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15342
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	240

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	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.