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Crystal Structure of symmetric swapped human Nck SH3.1 domain, 0.93A, orthorhombic form IV
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 7 293 60% tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.45 15.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.1 α = 90 b = 55.17 β = 90 c = 27 γ = 90
Symmetry Space Group P 21 21 2
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 2020-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00005 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 0.93 27.6 88.1 0.065 0.072 0.999 6.8 5.45 36162 17.679
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.93 1.06 63.6 14.779 17.331 0.17 3.539
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 0.93 27.6 18459 961 47.37 0.1506 0.1489 0.1821 0.1926 RANDOM 17.542
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] 1.35 -1.77 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.761 r_dihedral_angle_4_deg 32.824 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_1_deg 6.621 r_rigid_bond_restr 5.892 r_angle_refined_deg 1.842 r_angle_other_deg 1.44 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.761 r_dihedral_angle_4_deg 32.824 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_1_deg 6.621 r_rigid_bond_restr 5.892 r_angle_refined_deg 1.842 r_angle_other_deg 1.44 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 493 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing