4KYT | pdb_00004kyt

The structure of superinhibitory phospholamban bound to the calcium pump SERCA1a

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C8L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	1 ul of SERCA1a at 15 mg/mL in 2% n-nonyl-beta-D-maltopyranoside (nonyl maltoside) (Anatrace), 20% glycerol, 100 mM MOPS (pH 7.0), 0.12 M sucrose, 80 mM KCl, 3 mM MgCl2, and 2.8 mM EGTA was mixed with 1 uL of phospholamban at 2.1 mg/mL in 20 mM MOPS (pH 7.2), 20% glycerol, and 0.1 % decyl maltoside or 0.01% dodecyl maltoside. This protein mixture was then added to an equal volume of crystallization liquor; 15 % glycerol, 17% (W/V) PEG-2000, 200mM NaOAc, and 5 mM beta-mercoptoethanol), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.591	α = 90
b = 93.094	β = 90
c = 316.375	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		2013-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98	APS	19-ID

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	2.833	50	97.2	0.084	14.4	5.5	44230	42992	0.2	0.2	88.5

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	2.833	2.89	97.3		0.492	2.6	4.5	2106

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2c8l	2.833	50	0.2	42925	40758	2167	96.68	0.242	0.24139	0.23908	0.24	0.28388	0.28	RANDOM	92.343

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]
1.43			2.36		-3.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.324
r_dihedral_angle_4_deg	19.006
r_dihedral_angle_3_deg	18.303
r_dihedral_angle_1_deg	5.678
r_scangle_it	2.013
r_angle_refined_deg	1.196
r_scbond_it	1.172
r_mcangle_it	0.8
r_mcbond_it	0.409
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7861
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	47

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling