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YEAST SHO1 SH3 DOMAIN COMPLEXED WITH A PEPTIDE FROM PBS2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QK6 PDB ENTRY 2QK6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 2.3M AMMONIUM SULPHATE, 0.1M TRIS-HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.34 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.49 α = 90 b = 67.49 β = 90 c = 33.17 γ = 120
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 2006-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.05 20 99.7 0.08 14.8 5.5 5525 -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 2.05 2.1 100 0.62 2.8 5.5
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 2QK6 2.05 10 5233 243 99.8 0.171 0.168 0.1799 0.238 0.1757 RANDOM 28.6
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] 0.85 0.42 0.85 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.012 r_dihedral_angle_3_deg 18.186 r_dihedral_angle_4_deg 18.028 r_dihedral_angle_1_deg 6.575 r_scangle_it 4.746 r_scbond_it 3.389 r_mcangle_it 1.986 r_angle_refined_deg 1.444 r_mcbond_it 1.368 r_angle_other_deg 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.012 r_dihedral_angle_3_deg 18.186 r_dihedral_angle_4_deg 18.028 r_dihedral_angle_1_deg 6.575 r_scangle_it 4.746 r_scbond_it 3.389 r_mcangle_it 1.986 r_angle_refined_deg 1.444 r_mcbond_it 1.368 r_angle_other_deg 0.928 r_nbd_other 0.193 r_nbtor_refined 0.178 r_nbd_refined 0.167 r_symmetry_vdw_other 0.167 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_refined 0.138 r_symmetry_hbond_refined 0.118 r_nbtor_other 0.088 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 605 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing