3AR5

Calcium pump crystal structure with bound TNP-AMP and TG


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS6.1283pH 6.1, MICRODIALYSIS, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
3.4564.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.683α = 90
b = 71.683β = 90
c = 589.075γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.9SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.25099.48011279624-2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2699.60.4632.6788.15615

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1AGV2.215757787577840181000.261650.260250.28788RANDOM70.852
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]
0.320.32-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.844
r_dihedral_angle_4_deg21.661
r_dihedral_angle_3_deg18.057
r_dihedral_angle_1_deg5.676
r_scangle_it3.333
r_scbond_it1.993
r_mcangle_it1.705
r_angle_refined_deg1.453
r_mcbond_it0.92
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.844
r_dihedral_angle_4_deg21.661
r_dihedral_angle_3_deg18.057
r_dihedral_angle_1_deg5.676
r_scangle_it3.333
r_scbond_it1.993
r_mcangle_it1.705
r_angle_refined_deg1.453
r_mcbond_it0.92
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 AtomsNumber
Protein Atoms7674
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms142

Software

Software
Software NamePurpose
BSSdata collection
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing