3AR2 | pdb_00003ar2

Calcium pump crystal structure with bound AMPPCP and Ca2+

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.995	α = 90
b = 75.306	β = 108.97
c = 151.541	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	IMAGE PLATE	RIGAKU RAXIS V		2004-12-20	M	SINGLE WAVELENGTH

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 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	2.5	50	99.8	0.043	31.8	3.3	59902	59761		-3

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)
1	2.5	2.56	98.5		0.482	2.7	3	4201

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZBD	2.5	15	56359	56359	3001	100	0.24817	0.24688	0.24	0.27243	0.26	RANDOM	120.795

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]
-4.11		-5.28	11.64		-10.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.504
r_dihedral_angle_4_deg	18.971
r_dihedral_angle_3_deg	16.646
r_dihedral_angle_1_deg	3.348
r_scangle_it	2.556
r_mcangle_it	2.063
r_scbond_it	1.634
r_angle_refined_deg	1.252
r_mcbond_it	1.151
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7674
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	55

Software

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