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Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein in complex with a peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 2.9M sodium malonate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.08 40.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.92 α = 90 b = 33.92 β = 90 c = 113.1 γ = 90
Symmetry Space Group P 41 21 2
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 2004-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.9795 EMBL/DESY, HAMBURG BW7A
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 1.4 20 99.9 0.101 16.56 7.4 13804 -3 19.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.5 100
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 1OOT 1.4 18.82 13113 691 99.89 0.1652 0.16326 0.1884 0.2025 0.2248 RANDOM 6.76
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] -0.6 -0.6 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.772 r_scangle_it 3.652 r_scbond_it 2.355 r_mcangle_it 2.003 r_angle_refined_deg 1.558 r_mcbond_it 1.33 r_angle_other_deg 0.831 r_symmetry_vdw_other 0.308 r_nbd_other 0.251 r_symmetry_hbond_refined 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.772 r_scangle_it 3.652 r_scbond_it 2.355 r_mcangle_it 2.003 r_angle_refined_deg 1.558 r_mcbond_it 1.33 r_angle_other_deg 0.831 r_symmetry_vdw_other 0.308 r_nbd_other 0.251 r_symmetry_hbond_refined 0.202 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.199 r_chiral_restr 0.1 r_nbtor_other 0.086 r_symmetry_vdw_refined 0.071 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 556 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling AMoRE phasing