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Crystal Structure of the monomeric human Nck SH3.1 domain, triclinic, 1.08A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other inhouse model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 5-20 mg/mL protein in 25mM HEPES\/NaOH pH7.8, 150mM NaCl mixed 60-70% with 40-30% reservoir consisting of 0.1M BIS-TRIS\/HCl pH6.5, 2M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.77 30.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.91 α = 87.15 b = 28.37 β = 86.49 c = 38.56 γ = 67.04
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 PSI PILATUS 6M 2018-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99997 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.1 38.47 72.3 0.076 0.103 0.996 5.42 1.94 27558 14.129
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.13 15.3 1.022 1.406 0.354 0.61 1.79
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 inhouse model 1.08 38.47 19835 955 52.34 0.1611 0.1586 0.1663 0.2142 0.2213 RANDOM 8.783
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] 0.31 0.36 -0.19 -0.57 0.2 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.505 r_sphericity_free 22.945 r_dihedral_angle_4_deg 21.1 r_dihedral_angle_3_deg 13.657 r_sphericity_bonded 9.248 r_dihedral_angle_1_deg 7.424 r_rigid_bond_restr 3.018 r_angle_refined_deg 1.543 r_angle_other_deg 0.983 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.505 r_sphericity_free 22.945 r_dihedral_angle_4_deg 21.1 r_dihedral_angle_3_deg 13.657 r_sphericity_bonded 9.248 r_dihedral_angle_1_deg 7.424 r_rigid_bond_restr 3.018 r_angle_refined_deg 1.543 r_angle_other_deg 0.983 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 958 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 10
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing