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The second SH3 domain from Ponsin in complex with the paxillin proline rich region
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.2M Sodium Acetate, 0.1M Sodium Cacodylate, 30% (w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.74 29.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.49 α = 90 b = 41.852 β = 90 c = 58.79 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 2006-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8156 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 1.63 25 96.6 0.059 24 5 8022 7747 17.1
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) 1.63 1.66 80.5 0.221 4.2 2.7 380
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 2O2W 1.63 18.81 7500 218 100 0.1436 0.14255 0.1419 0.17686 0.1751 RANDOM 18.46
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] -0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 29.795 r_dihedral_angle_2_deg 28.449 r_dihedral_angle_3_deg 16.196 r_scangle_it 6.746 r_dihedral_angle_1_deg 5.878 r_scbond_it 4.62 r_mcangle_it 3.42 r_mcbond_it 2.193 r_angle_refined_deg 1.608 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 29.795 r_dihedral_angle_2_deg 28.449 r_dihedral_angle_3_deg 16.196 r_scangle_it 6.746 r_dihedral_angle_1_deg 5.878 r_scbond_it 4.62 r_mcangle_it 3.42 r_mcbond_it 2.193 r_angle_refined_deg 1.608 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.31 r_symmetry_hbond_refined 0.291 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.106 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 651 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing