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Structural basis of actin sequestration by thymosin-B4: Implications for arp2/3 activation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P8Z PDB ENTRY 1P8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 293 PEG 8000, Sodium acetate, calcium chloride, pH 6.5, microbatch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.85 α = 90 b = 69.335 β = 94.93 c = 80.233 γ = 90
Symmetry Space Group P 1 21 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0052 ESRF ID29
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 20 0.114 11.4 3.3 39223 39223
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) 2 2.1 0.198 3.6 3.3
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 1P8Z 2 20 39223 2079 98.15 0.14709 0.14445 0.1608 0.19531 0.2095 RANDOM 14.977
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] 1.14 0.35 -0.42 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.574 r_scangle_it 4.545 r_scbond_it 2.95 r_mcangle_it 1.629 r_angle_refined_deg 1.434 r_mcbond_it 0.969 r_angle_other_deg 0.868 r_symmetry_vdw_other 0.252 r_nbd_other 0.245 r_nbd_refined 0.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.574 r_scangle_it 4.545 r_scbond_it 2.95 r_mcangle_it 1.629 r_angle_refined_deg 1.434 r_mcbond_it 0.969 r_angle_other_deg 0.868 r_symmetry_vdw_other 0.252 r_nbd_other 0.245 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.094 r_nbtor_other 0.086 r_metal_ion_refined 0.078 r_symmetry_vdw_refined 0.068 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3959 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing