1TJX | pdb_00001tjx

Crystallographic Identification of Ca2+ Coordination Sites in Synaptotagmin I C2B Domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K5WPDB ENTRY 1K5W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15277ammonium sulfate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.00
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.55α = 90
b = 54.55β = 90
c = 103.59γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

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
11.0420990.10319.35.5585544
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)
11.041.0696.60.4161.62

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1K5W1.0419.585544812114278990.1670.1660.170.1840.2RANDOM12.29
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]
-0.48-0.24-0.480.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.204
r_sphericity_free4.943
r_scangle_it4.75
r_sphericity_bonded4.285
r_scbond_it3.02
r_mcangle_it2.672
r_mcbond_it1.752
r_angle_refined_deg1.714
r_rigid_bond_restr1.675
r_angle_other_deg1.433
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.204
r_sphericity_free4.943
r_scangle_it4.75
r_sphericity_bonded4.285
r_scbond_it3.02
r_mcangle_it2.672
r_mcbond_it1.752
r_angle_refined_deg1.714
r_rigid_bond_restr1.675
r_angle_other_deg1.433
r_symmetry_vdw_other0.316
r_symmetry_vdw_refined0.248
r_nbd_other0.245
r_nbd_refined0.215
r_symmetry_hbond_refined0.212
r_xyhbond_nbd_refined0.197
r_chiral_restr0.103
r_nbtor_other0.089
r_metal_ion_refined0.051
r_gen_planes_other0.02
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1228
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing