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Structure of the actin-depolymerizing factor homology domain in complex with actin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HD7 PDB ENTRY 2HD7, 2A42 experimental model PDB 2A42 PDB ENTRY 2HD7, 2A42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 10mM Tris pH 7.5, 50mM NaCl, 0.2mM ATP, 0.2mM DTT, 0.2mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.78 α = 90 b = 72.99 β = 90 c = 168.88 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 toroidal mirror 2007-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.072250 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.55 50 99.3 0.131 0.131 9.6 26755 26755
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.55 2.61 99.8 0.552 0.552 2.3 3.5 1318
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 2HD7, 2A42 2.55 42.76 20748 1125 99.31 0.21199 0.20821 0.2119 0.27925 0.2829 RANDOM 39.293
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] -0.29 0.16 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.478 r_dihedral_angle_3_deg 19.143 r_dihedral_angle_4_deg 18.187 r_dihedral_angle_1_deg 9.636 r_scangle_it 1.851 r_angle_refined_deg 1.534 r_scbond_it 1.214 r_mcangle_it 0.962 r_angle_other_deg 0.959 r_mcbond_it 0.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.478 r_dihedral_angle_3_deg 19.143 r_dihedral_angle_4_deg 18.187 r_dihedral_angle_1_deg 9.636 r_scangle_it 1.851 r_angle_refined_deg 1.534 r_scbond_it 1.214 r_mcangle_it 0.962 r_angle_other_deg 0.959 r_mcbond_it 0.556 r_symmetry_hbond_refined 0.244 r_symmetry_vdw_other 0.234 r_nbd_refined 0.221 r_nbd_other 0.199 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.153 r_metal_ion_refined 0.133 r_chiral_restr 0.091 r_nbtor_other 0.09 r_mcbond_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4056 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XDS data scaling PHASER phasing