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Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IOL PDB ENTRY 2IOL, chain A.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 10% (w/v) PEG-3000, 100 mM phosphate-citrate, 200 mM NaCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.254 α = 90 b = 64.021 β = 114.15 c = 38.453 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 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 0.97931 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 1.76 30 99.5 0.033 32.2 3.7 15015 14854 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) 1.76 1.806 95.6 0.248 4.54 3.3 1034
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2IOL, chain A. 1.76 30 15015 14183 754 99.48 0.212 0.19718 0.19459 0.1923 0.24853 0.2455 RANDOM 32.106
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] 0.5 -0.88 -0.23 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.718 r_dihedral_angle_4_deg 21.654 r_dihedral_angle_3_deg 13.629 r_scangle_it 5.534 r_dihedral_angle_1_deg 5.2 r_scbond_it 3.613 r_mcangle_it 2.233 r_angle_refined_deg 1.792 r_mcbond_it 1.578 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.718 r_dihedral_angle_4_deg 21.654 r_dihedral_angle_3_deg 13.629 r_scangle_it 5.534 r_dihedral_angle_1_deg 5.2 r_scbond_it 3.613 r_mcangle_it 2.233 r_angle_refined_deg 1.792 r_mcbond_it 1.578 r_nbtor_refined 0.308 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.239 r_symmetry_vdw_refined 0.231 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.115 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1013 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing