2ZBD | pdb_00002zbd

Crystal Structure of the SR Calcium Pump with Bound Aluminium Fluoride, ADP and Calcium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WPE	PDB ENTRY 1WPE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.1	283	PEG 400, pH 6.10, MICRODIALYSIS, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
4.01	69.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.9	α = 90
b = 75.1	β = 109.3
c = 152.1	γ = 90

Symmetry
Space Group	C 1 2 1

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		2005-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU		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	90.8	0.054	27.7	3.5		61807		-3

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)
	2.4	2.46	58.5		0.35	2.7	2.9

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-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1WPE	2.4	12	58529	58265	3093	100	0.24759	0.24633	0.27136	RANDOM	92.569

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]
-4.73		-5.97	12.1		-11.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.696
r_dihedral_angle_4_deg	16.924
r_dihedral_angle_3_deg	16.348
r_dihedral_angle_1_deg	4.722
r_angle_refined_deg	1.01
r_scangle_it	0.969
r_mcangle_it	0.607
r_scbond_it	0.602
r_mcbond_it	0.407
r_nbtor_refined	0.293
r_nbd_refined	0.182
r_xyhbond_nbd_refined	0.118
r_symmetry_hbond_refined	0.109
r_metal_ion_refined	0.096
r_symmetry_vdw_refined	0.094
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7671
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	147

Software

Software
Software Name	Purpose
CNS	refinement
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing