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Crystal Structure of STAM2 SH3 domain in complex with a UBPY-derived peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.08M Sodium Phosphate monobasic, 1.92M Potassium phosphate dibasic, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.29 45.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.454 α = 90 b = 48.454 β = 90 c = 58.582 γ = 120
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 RIGAKU 2002-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 34.1 97.9 8501 6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.79 96.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.7 34.11 8500 7602 898 97.62 0.2163 0.2163 0.21458 0.2159 0.22966 0.2302 RANDOM 25.802
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] 0.58 0.29 0.58 -0.87
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.352 r_dihedral_angle_1_deg 5.23 r_scbond_it 3.383 r_mcangle_it 2.58 r_angle_refined_deg 1.673 r_mcbond_it 1.458 r_symmetry_vdw_refined 0.27 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.352 r_dihedral_angle_1_deg 5.23 r_scbond_it 3.383 r_mcangle_it 2.58 r_angle_refined_deg 1.673 r_mcbond_it 1.458 r_symmetry_vdw_refined 0.27 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.215 r_chiral_restr 0.113 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 548 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling EPMR phasing