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Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 291 protein: 17.0 mg/mL in 20 mM Tris-HCl pH 7.3, 150 mM NaCl
well solution: 0.1M Tris-HCl pH 8.0, 1.6M LiS04 , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.03 59.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.806 α = 90 b = 88.117 β = 108.28 c = 90.226 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 180 CCD ADSC QUANTUM 315 2008-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97607 SSRL BL7-1
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 2.6 50 98.1 0.051 3.8 24012 24012 -3
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 2.6 2.69 97.9 0.58 1.8 3.9 2380
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.6 48 -3 21569 21569 2441 97.91 0.22355 0.21917 0.2142 0.26079 RANDOM 64.091
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.827 r_dihedral_angle_3_deg 18.512 r_dihedral_angle_4_deg 17.486 r_dihedral_angle_1_deg 5.592 r_mcangle_it 3.357 r_scangle_it 3.124 r_scbond_it 2.159 r_mcbond_it 2.141 r_angle_refined_deg 1.131 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.827 r_dihedral_angle_3_deg 18.512 r_dihedral_angle_4_deg 17.486 r_dihedral_angle_1_deg 5.592 r_mcangle_it 3.357 r_scangle_it 3.124 r_scbond_it 2.159 r_mcbond_it 2.141 r_angle_refined_deg 1.131 r_nbtor_refined 0.302 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.12 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4466 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing