☰ Navigation Tabs
Structure of the yeast YHH6 SH3 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OOT PDB Entry: 1OOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2.4 M ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.83 α = 90 b = 66.83 β = 90 c = 52.68 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 2004-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9537 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.54 40 98.1 0.06 15.5 4.4 19553 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.54 1.6 93.6 0.307 4.6 3.4
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: 1OOT 1.54 33.41 18569 977 98.28 0.17329 0.17109 0.2059 0.21547 0.1997 RANDOM 10.595
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] 0.11 0.05 0.11 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.027 r_scangle_it 3.222 r_scbond_it 2.198 r_mcangle_it 1.865 r_angle_refined_deg 1.454 r_mcbond_it 1.248 r_angle_other_deg 0.811 r_symmetry_vdw_other 0.333 r_symmetry_vdw_refined 0.294 r_nbd_other 0.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.027 r_scangle_it 3.222 r_scbond_it 2.198 r_mcangle_it 1.865 r_angle_refined_deg 1.454 r_mcbond_it 1.248 r_angle_other_deg 0.811 r_symmetry_vdw_other 0.333 r_symmetry_vdw_refined 0.294 r_nbd_other 0.254 r_xyhbond_nbd_refined 0.223 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.19 r_chiral_restr 0.095 r_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 920 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing