2O9J

Crystal structure of calcium atpase with bound magnesium fluoride and cyclopiazonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WPGpdb entry 1WPG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.12848% PEG 3350, 21% glycerol, 20mM MgCl2, 0.1mM EGTA, 20 mM MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties
Matthews coefficientSolvent content
3.8367.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.383α = 90
b = 69.875β = 107.1
c = 143.411γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 12.3.1ALS12.3.1

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
12.653099.70.063154486602
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)
12.652.741000.51144855

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 1WPG2.6529.148429242199.670.2480.2460.287RANDOM83.564
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]
-0.21-0.24-0.060.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.344
r_dihedral_angle_3_deg16.434
r_dihedral_angle_4_deg16.042
r_dihedral_angle_1_deg4.417
r_scangle_it1.55
r_angle_refined_deg1.28
r_scbond_it0.886
r_mcangle_it0.831
r_mcbond_it0.447
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.344
r_dihedral_angle_3_deg16.434
r_dihedral_angle_4_deg16.042
r_dihedral_angle_1_deg4.417
r_scangle_it1.55
r_angle_refined_deg1.28
r_scbond_it0.886
r_mcangle_it0.831
r_mcbond_it0.447
r_nbtor_refined0.323
r_symmetry_hbond_refined0.263
r_nbd_refined0.225
r_symmetry_vdw_refined0.216
r_xyhbond_nbd_refined0.194
r_metal_ion_refined0.114
r_chiral_restr0.076
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7562
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms32

Software

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