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Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form2
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 4.6 293 0.17 M ammonium sulfate, 0.085 M sodium acetate, 25.5% (w/v) PEG 2000 MME, 15% (v/v) glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.536 α = 90 b = 61.536 β = 90 c = 78.066 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 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
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 1.57 30 99.6 0.08 20.6 5.1 24343 23715 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 1.571 1.612 95.45 0.501 3.2 4.6 1605
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 1.57 30 24343 23008 1241 99.56 0.183 0.1615 0.15974 0.1744 0.1948 0.205 RANDOM 15.253
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] 0.52 0.26 0.52 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.605 r_dihedral_angle_4_deg 23.201 r_dihedral_angle_3_deg 11.118 r_scangle_it 4.587 r_dihedral_angle_1_deg 4.346 r_scbond_it 3.002 r_mcangle_it 1.889 r_angle_refined_deg 1.78 r_mcbond_it 1.591 r_angle_other_deg 0.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.605 r_dihedral_angle_4_deg 23.201 r_dihedral_angle_3_deg 11.118 r_scangle_it 4.587 r_dihedral_angle_1_deg 4.346 r_scbond_it 3.002 r_mcangle_it 1.889 r_angle_refined_deg 1.78 r_mcbond_it 1.591 r_angle_other_deg 0.968 r_mcbond_other 0.381 r_symmetry_hbond_refined 0.322 r_nbd_refined 0.252 r_symmetry_vdw_other 0.244 r_xyhbond_nbd_refined 0.218 r_nbtor_refined 0.185 r_nbd_other 0.175 r_symmetry_vdw_refined 0.174 r_chiral_restr 0.105 r_nbtor_other 0.084 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1036 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing