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Crystal structure of human TBC1 domain family member 7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 20% PEG-1500, 0.2M magnesium chloride, 0.1M TRIS. 1:10 dispase-1 added in situ., pH 8.5, vapor diffusion, sitting drop, temperature 289K 2 VAPOR DIFFUSION, SITTING DROP 7.5 289 Selenomethionyl derivative protein. 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES. 1:10 dispase-1 added in situ., pH 7.5, vapor diffusion, sitting drop, temperature 289K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.574 α = 90 b = 83.984 β = 90 c = 87.684 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 CCD ADSC QUANTUM 315 2011-02-10 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 315 2011-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID 2 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 APS 19-ID
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 1,2 1.9 40 99.7 0.066 11.4 7 21049
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) 1,2 1.9 1.97 100 0.855 7.1 2072
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.9 30 20715 1062 99.348 0.213 0.2112 0.2129 0.2585 0.2504 RANDOM 31.721
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] 0.907 -1.934 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.259 r_dihedral_angle_4_deg 26.469 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_1_deg 5.042 r_scangle_it 3.491 r_scbond_it 2.161 r_angle_refined_deg 1.322 r_mcangle_it 1.298 r_angle_other_deg 0.92 r_mcbond_it 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.259 r_dihedral_angle_4_deg 26.469 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_1_deg 5.042 r_scangle_it 3.491 r_scbond_it 2.161 r_angle_refined_deg 1.322 r_mcangle_it 1.298 r_angle_other_deg 0.92 r_mcbond_it 0.68 r_mcbond_other 0.171 r_chiral_restr 0.075 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2134 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling