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Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein at 1.39 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 295 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.98 37.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.93 α = 90 b = 39.93 β = 90 c = 69.49 γ = 120
Symmetry Space Group P 31 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 MARRESEARCH 2003-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8028 EMBL/DESY, HAMBURG X13
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 1.38 30 97 0.056 15 5.5 13185 13185 -3 21.65
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) 1.38 1.44 88.1 0.414 2.7 3.1 1398
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 1SEM 1.39 20 13120 13120 656 97.76 0.13397 0.13397 0.13207 0.1349 0.17046 0.1672 RANDOM 15.044
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] 1.17 0.58 1.17 -1.75
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 7.14 r_scangle_it 5.918 r_dihedral_angle_1_deg 5.179 r_sphericity_bonded 5.126 r_mcangle_it 4.075 r_scbond_it 3.992 r_mcbond_it 2.991 r_rigid_bond_restr 2.246 r_angle_refined_deg 1.842 r_angle_other_deg 0.879
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 7.14 r_scangle_it 5.918 r_dihedral_angle_1_deg 5.179 r_sphericity_bonded 5.126 r_mcangle_it 4.075 r_scbond_it 3.992 r_mcbond_it 2.991 r_rigid_bond_restr 2.246 r_angle_refined_deg 1.842 r_angle_other_deg 0.879 r_symmetry_vdw_other 0.366 r_symmetry_hbond_refined 0.258 r_nbd_other 0.246 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.114 r_nbtor_other 0.09 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 515 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AMoRE phasing