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The crystal structure of human synapsin III (SYN3) in complex with AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I7L Swissmodel based on PDB entries: 1I7L, 1I7N, 1PK8 experimental model PDB 1I7N Swissmodel based on PDB entries: 1I7L, 1I7N, 1PK8 experimental model PDB 1PK8 Swissmodel based on PDB entries: 1I7L, 1I7N, 1PK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 1.26M (NH4)2SO4, 0.2M Li2SO4, Tris-HCl pH 8.5, 20 % Ethylene glycol added as cryoprotectant, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.796 α = 90 b = 73.186 β = 100.74 c = 78.398 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD 2006-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99991 SLS X10SA
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 1.9 64.28 99.2 0.132 3.5 56940 56940
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 1.9 2 94.4 0.477 2.3
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 (All) 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 Swissmodel based on PDB entries: 1I7L, 1I7N, 1PK8 1.9 47 54131 54131 2801 99.15 0.18311 0.18311 0.18131 0.1861 0.21804 0.2214 RANDOM 19.433
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] -0.93 0.57 0.75 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.633 r_dihedral_angle_4_deg 19.816 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_1_deg 6.23 r_scangle_it 2.419 r_scbond_it 1.703 r_angle_refined_deg 1.358 r_mcangle_it 1.01 r_angle_other_deg 0.882 r_mcbond_it 0.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.633 r_dihedral_angle_4_deg 19.816 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_1_deg 6.23 r_scangle_it 2.419 r_scbond_it 1.703 r_angle_refined_deg 1.358 r_mcangle_it 1.01 r_angle_other_deg 0.882 r_mcbond_it 0.741 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.192 r_nbd_other 0.19 r_symmetry_vdw_other 0.183 r_nbtor_refined 0.177 r_mcbond_other 0.171 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.159 r_nbtor_other 0.085 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4651 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing