4Y3U | pdb_00004y3u

The structure of phospholamban bound to the calcium pump SERCA1a

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KYT	PDB entry 4KYT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	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 % DECYLMALTOSIDE 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)

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.745	α = 90
b = 91.825	β = 90
c = 316.256	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 315r		2013-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.987	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	3.5	50	99	0.087	16.46	4.7		23282	0.2	0.2

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	3.5	3.56	100		0.543	2.47	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 4KYT	3.51	48.79	22031	1195	98.91	0.23697	0.23478	0.23	0.27735	0.27	RANDOM	135.931

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]
1.54			1.61		-3.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.734
r_dihedral_angle_3_deg	18.114
r_dihedral_angle_4_deg	13.558
r_long_range_B_refined	8.479
r_dihedral_angle_1_deg	5.277
r_mcangle_it	4.291
r_scbond_it	2.643
r_mcbond_it	2.509
r_angle_refined_deg	1.021
r_chiral_restr	0.068
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7811
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1

Software

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