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sh2 domain of human nck1 adaptor protein - uncomplexed
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JYU PDB ENTRY 1JYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 METHOD: HANGING-DROP, VAPOR-DIFFUSION AT 4 DEGREES C, PROTEIN: 8 MG/ML PROTEIN IN 20 MM TRIS/HCL, PH 8.0, RESERVOIR: 25% PEG5000 MME, 0.1M MES PH 6.5, 0.2M (NH4)2SO4, 0.1M GUANIDINE HCL. CRYOPROTECTANT: 20% MPD
Crystal Properties Matthews coefficient Solvent content 2.46 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.854 α = 90 b = 82.484 β = 90 c = 44.538 γ = 90
Symmetry Space Group C 2 2 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 CCD MARRESEARCH 2003-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.8 30 99.1 0.05 34.3 6.1 11119
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 1.8 1.85 95.5 0.37 3.2 4.6
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 PDB ENTRY 1JYU 1.8 30.26 10457 526 99.2 0.232 0.23 0.2333 0.274 0.2653 RANDOM 25.14
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.956 r_dihedral_angle_3_deg 16.166 r_dihedral_angle_4_deg 12.242 r_dihedral_angle_1_deg 5.456 r_angle_other_deg 3.305 r_angle_refined_deg 1.813 r_chiral_restr 0.393 r_symmetry_hbond_refined 0.284 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.956 r_dihedral_angle_3_deg 16.166 r_dihedral_angle_4_deg 12.242 r_dihedral_angle_1_deg 5.456 r_angle_other_deg 3.305 r_angle_refined_deg 1.813 r_chiral_restr 0.393 r_symmetry_hbond_refined 0.284 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.204 r_symmetry_vdw_other 0.201 r_nbtor_refined 0.2 r_nbd_other 0.18 r_symmetry_vdw_refined 0.171 r_nbtor_other 0.151 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.003 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 805 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing