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rat synaptotagmin 4 C2B domain in the absence of calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K5W PDB ENTRY 1K5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 THE 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 4.25 M NACL, 0.1 M HEPES PH 7.5 AND 5%(V/V) ETHYLENE GLYCOL AND THEN COOLED IN LIQUID PROPANE.
Crystal Properties Matthews coefficient Solvent content 4.4 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.061 α = 90 b = 91.061 β = 90 c = 122.86 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD CUSTOM 2003-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 29.81 99.6 0.053 45.8 11.4 13974 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 95.2 0.725 1.8 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1K5W 2.3 30 12558 1392 99.6 0.217 0.213 0.2197 0.257 RANDOM 55.09
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] 1.02 0.51 1.02 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_3_deg 18.583 r_dihedral_angle_4_deg 15.413 r_dihedral_angle_1_deg 7.423 r_scangle_it 4.815 r_scbond_it 3.114 r_mcangle_it 2.247 r_angle_refined_deg 1.851 r_mcbond_it 1.216 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_3_deg 18.583 r_dihedral_angle_4_deg 15.413 r_dihedral_angle_1_deg 7.423 r_scangle_it 4.815 r_scbond_it 3.114 r_mcangle_it 2.247 r_angle_refined_deg 1.851 r_mcbond_it 1.216 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.246 r_symmetry_hbond_refined 0.229 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.115 r_metal_ion_refined 0.053 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 992 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing