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Crystal structure of the second SH3 domain from ponsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 15% v/v Tascinamine, 0.1M HEPES, 2% w/v PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.02 38.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.661 α = 90 b = 35.499 β = 90 c = 71.079 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2005-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8125 EMBL/DESY, HAMBURG X11
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 14 99.6 0.065 23.1 5.9 10752 10707 10.754
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) 1.49 1.52 100 0.229 7.8 5.8 515
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 1W70 1.5 13.36 10124 311 100 0.13195 0.13114 0.1368 0.16182 0.1651 RANDOM 14.822
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] 0.44 -0.81 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.988 r_sphericity_free 11.895 r_dihedral_angle_4_deg 10.767 r_dihedral_angle_3_deg 10.699 r_dihedral_angle_1_deg 6.416 r_sphericity_bonded 5.45 r_scangle_it 4.794 r_scbond_it 3.716 r_mcangle_it 2.637 r_rigid_bond_restr 2.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.988 r_sphericity_free 11.895 r_dihedral_angle_4_deg 10.767 r_dihedral_angle_3_deg 10.699 r_dihedral_angle_1_deg 6.416 r_sphericity_bonded 5.45 r_scangle_it 4.794 r_scbond_it 3.716 r_mcangle_it 2.637 r_rigid_bond_restr 2.077 r_mcbond_it 1.882 r_angle_refined_deg 1.611 r_nbtor_refined 0.32 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.122 r_symmetry_hbond_refined 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 553 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing