1W15

rat synaptotagmin 4 C2B domain in the presence of calcium


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5THE RAT SYNAPTOTAGMIN IV C2B DOMAIN WAS CRYSTALLIZED BY THE VAPOR DIFFUSION METHOD (HANGING DROP) BY MIXING 1 MICROLITER PROTEIN (IN 20 MM MES, 150 MM NACL AND 1 MM EDTA, PH 6.32) WITH 1 MICROLITER RESERVOIR SOLUTION (2.5M NACL, 0.1M CACL2, 0.1M HEPES, PH 7.5) SUSPENDED OVER 500 MICROLITERS RESERVOIR SOLUTION. HEXAGONAL CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF 0.1 X 0.1 X 0.2 MM WITHIN TWO DAYS. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO CRYSTALLIZATION SOLUTION CONTAINING 20% (V/V) ETHYLENE GLYCOL FOR CRYSTALS GROWN IN 0.1 M CACL2, AND THEN COOLED IN LIQUID PROPANE.
Crystal Properties
Matthews coefficientSolvent content
4.472.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.49α = 90
b = 91.49β = 90
c = 122.142γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM2003-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-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
11.9337.68499.90.05441.511.923368-3
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)
11.931.9699.90.7192.38.5

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 1K5W1.933021854147599.90.2060.2040.233RANDOM42.85
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]
0.260.130.26-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.182
r_dihedral_angle_3_deg15.78
r_dihedral_angle_4_deg12.574
r_dihedral_angle_1_deg6.377
r_scangle_it5.166
r_scbond_it3.159
r_mcangle_it2.218
r_angle_refined_deg1.821
r_mcbond_it1.214
r_nbtor_refined0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.182
r_dihedral_angle_3_deg15.78
r_dihedral_angle_4_deg12.574
r_dihedral_angle_1_deg6.377
r_scangle_it5.166
r_scbond_it3.159
r_mcangle_it2.218
r_angle_refined_deg1.821
r_mcbond_it1.214
r_nbtor_refined0.332
r_nbd_refined0.26
r_symmetry_vdw_refined0.215
r_symmetry_hbond_refined0.209
r_xyhbond_nbd_refined0.2
r_metal_ion_refined0.152
r_chiral_restr0.151
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1046
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling