3NAM | pdb_00003nam

SR Ca(2+)-ATPase in the HnE2 state complexed with the Thapsigargin derivative dOTg

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C8K	PDB ENTRY 2C8K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	8% w/v PEG 2000 MME, 4% v/v glycerol, 0.05M NaCl, 4% v/v 2-methyl-2,4-pentanediol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.545	α = 90
b = 71.545	β = 90
c = 591.227	γ = 90

Symmetry
Space Group	P 41 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		2005-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.2548	SLS	X06SA

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	3.1	30	90.6	0.168	11.18	5.2	29674	26884	-3	-3	72.4

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)
	3.1	3.21	75.4		0.579	1.9	3.4

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-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 2C8K	3.1	30	29674	26087	735	88.4	0.239	0.2324	0.28	0.24	random	95.939

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]
6.481			6.481		-12.962

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.095
c_mcangle_it	2.47
c_scbond_it	1.875
c_mcbond_it	1.383

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7671
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	62

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
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.