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1.15 Angstrom Crystal Structure of the MA3 domain of Pdcd4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ION PDB ENTRY 2ION
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 2.83 56.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.52 α = 90 b = 61.52 β = 90 c = 77.751 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 MAR CCD 165 mm 2006-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 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 1.15 28.6 97 0.06 28.2 7.1 61054 59292 1 17.4
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 1.15 1.18 99.91 0.465 4.54 7 4263
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ION 1.15 28.6 57917 3093 99.94 0.13316 0.13228 0.132 0.14959 0.1479 RANDOM 10.826
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] 0.19 0.1 0.19 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.557 r_dihedral_angle_4_deg 16.331 r_dihedral_angle_3_deg 10.902 r_sphericity_free 6.354 r_dihedral_angle_1_deg 4.14 r_scangle_it 4.036 r_sphericity_bonded 3.496 r_scbond_it 2.974 r_mcangle_it 2.104 r_mcbond_it 1.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.557 r_dihedral_angle_4_deg 16.331 r_dihedral_angle_3_deg 10.902 r_sphericity_free 6.354 r_dihedral_angle_1_deg 4.14 r_scangle_it 4.036 r_sphericity_bonded 3.496 r_scbond_it 2.974 r_mcangle_it 2.104 r_mcbond_it 1.717 r_rigid_bond_restr 1.491 r_angle_refined_deg 1.451 r_angle_other_deg 0.864 r_mcbond_other 0.598 r_symmetry_hbond_refined 0.358 r_symmetry_vdw_other 0.25 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.228 r_nbtor_refined 0.186 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.096 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement