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Crystal structure of the Habc domain of neuronal syntaxin from the squid Loligo pealei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EZ3 pdb entry 1EZ3, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG 400, 0.2M Na-citrate, 0.1M Tris HCl, 20mM HEPES-KOH, 100mM KCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.74 66.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.056 α = 90 b = 73.056 β = 90 c = 224.434 γ = 90
Symmetry Space Group P 43 21 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 ADSC QUANTUM 4 2001-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0088 ESRF ID29
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 3.3 15 99.4 0.074 14.8 6.4 9361 9304
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 3.3 3.42 100 0.375 4.6 906
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1EZ3, chain A 3.34 14.97 8751 8751 500 100 0.31255 0.30878 0.2918 0.37537 0.3364 RANDOM 42.344
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] -1.79 -1.79 3.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.636 r_scangle_it 3.478 r_scbond_it 1.84 r_angle_refined_deg 1.61 r_mcangle_it 1.328 r_angle_other_deg 0.959 r_mcbond_it 0.684 r_nbd_refined 0.315 r_symmetry_vdw_refined 0.276 r_nbd_other 0.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.636 r_scangle_it 3.478 r_scbond_it 1.84 r_angle_refined_deg 1.61 r_mcangle_it 1.328 r_angle_other_deg 0.959 r_mcbond_it 0.684 r_nbd_refined 0.315 r_symmetry_vdw_refined 0.276 r_nbd_other 0.254 r_symmetry_vdw_other 0.216 r_xyhbond_nbd_refined 0.172 r_nbtor_other 0.09 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1620 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing