☰ Navigation Tabs
Crystal structure of PDZ domain of Synaptojanin-2 binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FE5 PDB ENTRY 2FE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 30% PEG10K, 0.20M LITHIUM SULPHATE, 0.1M ACETATE PH 4.5
Crystal Properties Matthews coefficient Solvent content 2.02 39.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.993 α = 90 b = 65.993 β = 90 c = 41.384 γ = 90
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 MARRESEARCH 2007-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 1.5 46.68 99.7 0.08 12.6 4.5 14288 14.38
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 1.5 1.58 97.6 0.52 2.1 2.6
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2FE5 1.5 46.68 13546 716 99.5 0.169 0.166 0.1711 0.22 0.2173 RANDOM 15.86
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] 0.05 0.05 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.904 r_dihedral_angle_4_deg 13.291 r_dihedral_angle_3_deg 11.427 r_scangle_it 8.12 r_dihedral_angle_1_deg 5.88 r_scbond_it 5.8 r_mcangle_it 3.605 r_mcbond_it 2.424 r_angle_other_deg 2.029 r_angle_refined_deg 1.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.904 r_dihedral_angle_4_deg 13.291 r_dihedral_angle_3_deg 11.427 r_scangle_it 8.12 r_dihedral_angle_1_deg 5.88 r_scbond_it 5.8 r_mcangle_it 3.605 r_mcbond_it 2.424 r_angle_other_deg 2.029 r_angle_refined_deg 1.418 r_symmetry_vdw_other 0.307 r_nbd_refined 0.249 r_symmetry_vdw_refined 0.226 r_nbd_other 0.214 r_symmetry_hbond_refined 0.202 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.135 r_nbtor_other 0.095 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 780 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing