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Crystal Structure of domain swapped human Nck SH3.1, 1.01A, monoclinic
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 5.5 293 0.1 M Tris/HCl pH 8.0, 0.15 M NaCl, 8% PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.66 25.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.453 α = 90 b = 55.723 β = 98.7 c = 39.924 γ = 90
Symmetry Space Group P 1 21 1
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 2018-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 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 1.02 32.23 91.8 0.049 0.054 0.999 9.88 4.84 59526 17.574
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 1.02 1.05 73.4 3.718 4.264 0.181 0.29 4.047
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 inhouse model 1.02 32.23 38767 2101 62.77 0.1645 0.1632 0.1888 0.198 RANDOM 13.641
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] -0.93 0.1 0.34 0.54
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.203 r_dihedral_angle_2_deg 31.528 r_dihedral_angle_4_deg 24.784 r_dihedral_angle_3_deg 11.786 r_sphericity_bonded 11.113 r_dihedral_angle_1_deg 7.473 r_rigid_bond_restr 2.945 r_angle_refined_deg 1.636 r_angle_other_deg 0.999 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.203 r_dihedral_angle_2_deg 31.528 r_dihedral_angle_4_deg 24.784 r_dihedral_angle_3_deg 11.786 r_sphericity_bonded 11.113 r_dihedral_angle_1_deg 7.473 r_rigid_bond_restr 2.945 r_angle_refined_deg 1.636 r_angle_other_deg 0.999 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 960 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing