3F00

Crystal Structure of Synaptotagmin I C2A domain with Cu(II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RSYPDB entry 1RSY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52982.0M Li2SO4, 100mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1843.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.647α = 90
b = 38.363β = 98.37
c = 44.016γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2005-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.98268APS19-BM

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
11.3610095.60.16515.7864.128585
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)
1.361.4173.20.5142.22177

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 1RSY1.3620.628466141499.280.2030.2010.244RANDOM17.97
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.043
r_dihedral_angle_3_deg10.123
r_dihedral_angle_4_deg5.777
r_dihedral_angle_1_deg3.875
r_sphericity_bonded3.782
r_sphericity_free3.142
r_mcangle_it2.099
r_scangle_it1.851
r_mcbond_it1.397
r_scbond_it1.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.043
r_dihedral_angle_3_deg10.123
r_dihedral_angle_4_deg5.777
r_dihedral_angle_1_deg3.875
r_sphericity_bonded3.782
r_sphericity_free3.142
r_mcangle_it2.099
r_scangle_it1.851
r_mcbond_it1.397
r_scbond_it1.294
r_angle_refined_deg1.253
r_rigid_bond_restr1.159
r_nbtor_refined0.324
r_nbd_refined0.284
r_symmetry_vdw_refined0.257
r_xyhbond_nbd_refined0.227
r_symmetry_hbond_refined0.195
r_symmetry_metal_ion_refined0.12
r_metal_ion_refined0.119
r_chiral_restr0.086
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1166
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing