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Crystal structure of APPL1 PTB domain at 1.8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 100mM Na Citrate, 10% PEG 3350, 15% Isopropanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.23 α = 90 b = 63.566 β = 102.67 c = 52.449 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 210 2006-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.97900 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.84 50 97.3 0.104 0.103 9.59801 3.5652 24816 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.84 1.92 91.4 0.455 0.331 2.73783 2.5 1784
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 1.84 50 3 23949 1280 99.79 0.19526 0.19332 0.2081 0.23014 0.2141 RANDOM 23.701
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] -0.7 -1.48 0.16 -0.12
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.408 r_dihedral_angle_1_deg 5.684 r_scbond_it 3.793 r_mcangle_it 2.797 r_mcbond_it 1.476 r_angle_refined_deg 1.438 r_angle_other_deg 0.805 r_nbd_refined 0.364 r_symmetry_hbond_refined 0.263 r_symmetry_vdw_other 0.257
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.408 r_dihedral_angle_1_deg 5.684 r_scbond_it 3.793 r_mcangle_it 2.797 r_mcbond_it 1.476 r_angle_refined_deg 1.438 r_angle_other_deg 0.805 r_nbd_refined 0.364 r_symmetry_hbond_refined 0.263 r_symmetry_vdw_other 0.257 r_nbd_other 0.253 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.094 r_nbtor_other 0.082 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2105 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling SnB phasing