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Crystal structure of the second SH3 domain of FCHSD2 (SH3-2) in complex with the fourth SH3 domain of ITSN1 (SH3d)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DL7 2DL7, 1UE9 experimental model PDB 1UE9 2DL7, 1UE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.5M ammonium sulfate, 10% Glycerol, Tris pH8.5
Crystal Properties Matthews coefficient Solvent content 4.76 74.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.984 α = 90 b = 186.984 β = 90 c = 186.984 γ = 90
Symmetry Space Group I 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 3.44 132.2 99.4 0.053 27.1 8.4 13008
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 3.44 3.53
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DL7, 1UE9 3.44 132.2 13008 1437 99.32 0.2118 0.20788 0.24673 0.2333 RANDOM 142.45
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.316 r_dihedral_angle_4_deg 25.883 r_long_range_B_other 20.979 r_long_range_B_refined 20.978 r_mcangle_it 17.379 r_mcangle_other 17.378 r_scangle_other 17.317 r_dihedral_angle_3_deg 17.262 r_mcbond_it 11.705 r_mcbond_other 11.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.316 r_dihedral_angle_4_deg 25.883 r_long_range_B_other 20.979 r_long_range_B_refined 20.978 r_mcangle_it 17.379 r_mcangle_other 17.378 r_scangle_other 17.317 r_dihedral_angle_3_deg 17.262 r_mcbond_it 11.705 r_mcbond_other 11.7 r_scbond_other 11.633 r_scbond_it 11.632 r_dihedral_angle_1_deg 7.214 r_angle_other_deg 3.858 r_angle_refined_deg 1.512 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3581 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing