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Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG 1000, 0.1 M HEPES, 5% GLYCEROL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.33 63.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.65 α = 90 b = 64.65 β = 90 c = 164.7 γ = 120
Symmetry Space Group P 31 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 100 CCD MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97174 APS 22-ID
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 30 98 0.1 15.1 4.7 27732 26640 1 1
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 2.001 2.053 95.93 0.58 1.96 3.3 1818
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 (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 SAD THROUGHOUT 2 30 1 26640 25810 1381 98.05 0.357 0.26056 0.25868 0.2568 0.29734 0.295 RANDOM 51.668
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] -0.07 -0.04 -0.07 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.65 r_dihedral_angle_3_deg 17.353 r_dihedral_angle_4_deg 14.802 r_dihedral_angle_1_deg 5.133 r_scangle_it 3.483 r_scbond_it 2.354 r_angle_refined_deg 1.482 r_mcangle_it 1.235 r_mcbond_it 0.932 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.65 r_dihedral_angle_3_deg 17.353 r_dihedral_angle_4_deg 14.802 r_dihedral_angle_1_deg 5.133 r_scangle_it 3.483 r_scbond_it 2.354 r_angle_refined_deg 1.482 r_mcangle_it 1.235 r_mcbond_it 0.932 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.238 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.209 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2060 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing