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Crystal structure of conserved motif in TDRD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 291 crystal used for final refinement: 1.5 M ammonium phosphate, 0.1 M bis-tris propane. 1:200 trypsin was also added., pH 8.5, vapor diffusion, temperature 291K 2 291 Selenomethionyl derivative: 1.5 M ammonium phosphat
e, 0.1 M bis-tris propane. 1:200 trypsin was also added., pH 7, vapor diffusion, temperature 291K 3 291 crystal used for preliminary refinement: 25 w/v% PEG-3350, 0.2 M lithium sulfate, 0.1 M bis-tris propane. 1:200 trypsin was also added., pH 6.5, vapor diffusion, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.94 α = 90 b = 43.33 β = 90 c = 126.6 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 RIGAKU SATURN 2011-04-18 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC Q210 BINNED 2011-05-11 M SINGLE WAVELENGTH 3 3 x-ray 100 CCD MAR 300 2011-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 2 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1 3 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-1
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 2.28 30 94.8 0.038 33.8 10833 -3 50.51
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 2.28 2.34 76.9 0.791 2.8
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 2.28 27.48 10803 575 0.246 0.245 0.2569 0.271 0.2605 THIN SHELLS (SFTOOLS) 48.56
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] 2.5105 -3.3032 0.7928
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.08 t_omega_torsion 2.61 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.08 t_omega_torsion 2.61 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1197 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 8
Software Software Software Name Purpose XSCALE data scaling SOLVE phasing RESOLVE phasing BUSTER-TNT refinement PDB_EXTRACT data extraction BUSTER refinement