2OA0

Crystal structure of Calcium ATPase with bound ADP and cyclopiazonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AGVpdb entry 2AGV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.12842.75-3% PEG3350, 25% glycerol, 20 mM MgCl2, 0.1mM EGTA, 20 mM MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties
Matthews coefficientSolvent content
4.2671.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.498α = 90
b = 96.836β = 94.83
c = 154.856γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-05-26MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 2102005-06-16MSINGLE WAVELENGTH
31x-ray100CCDADSC QUANTUM 3152005-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11587ALS8.3.1
2SYNCHROTRONALS BEAMLINE 8.3.11.11698ALS8.3.1
3SYNCHROTRONALS BEAMLINE 8.2.21.0ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,2,33.4301000.1199.512.4254272
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.43.5299.80.7047.12508

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2AGV3.43025372126599.490.2920.290.328RANDOM122.587
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]
-0.270.432.55-2.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.703
r_dihedral_angle_3_deg19.446
r_dihedral_angle_4_deg17.94
r_dihedral_angle_1_deg4.677
r_angle_refined_deg1.274
r_symmetry_vdw_refined0.351
r_nbtor_refined0.332
r_nbd_refined0.262
r_xyhbond_nbd_refined0.196
r_symmetry_hbond_refined0.166
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.703
r_dihedral_angle_3_deg19.446
r_dihedral_angle_4_deg17.94
r_dihedral_angle_1_deg4.677
r_angle_refined_deg1.274
r_symmetry_vdw_refined0.351
r_nbtor_refined0.332
r_nbd_refined0.262
r_xyhbond_nbd_refined0.196
r_symmetry_hbond_refined0.166
r_chiral_restr0.084
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7562
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms53

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction