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Crystal Structure of Monobody HA4/Abl1 SH2 Domain Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OPK 1OPK: 154-235, 1FNF: loops omitted experimental model PDB 1FNF 1OPK: 154-235, 1FNF: loops omitted
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG 4000, 0.2M sodium acetate trihydrate, 0.1M Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.625 α = 90 b = 88.181 β = 90 c = 131.081 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2008-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97872 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.751 50 95.3 0.046 6.1 38402 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.751 1.81 65 0.438 1.9 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1OPK: 154-235, 1FNF: loops omitted 1.75 39 2 40297 38402 1922 95.3 0.183 0.182 0.18 0.1814 0.221 0.2228 RANDOM 27.667
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] -0.76 -0.18 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 19.742 r_dihedral_angle_3_deg 11.706 r_dihedral_angle_1_deg 5.955 r_scangle_it 2.935 r_scbond_it 2.27 r_angle_refined_deg 1.5 r_mcangle_it 1.482 r_mcbond_it 0.934 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 19.742 r_dihedral_angle_3_deg 11.706 r_dihedral_angle_1_deg 5.955 r_scangle_it 2.935 r_scbond_it 2.27 r_angle_refined_deg 1.5 r_mcangle_it 1.482 r_mcbond_it 0.934 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.196 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3089 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling