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The structure of Aplyronine A-actin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG8000 20%(w/v) 0.1M sodium cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.704 α = 90 b = 75.123 β = 95.23 c = 67.546 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 IMAGE PLATE RIGAKU RAXIS V 2004-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.45 35.53 100 69927
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 (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 1eqy 1.45 35.53 66395 3532 100 0.15266 0.15266 0.15135 0.1515 0.17579 0.1775 RANDOM 15.878
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] 0.03 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.319 r_dihedral_angle_4_deg 15.642 r_dihedral_angle_3_deg 12.547 r_dihedral_angle_1_deg 5.289 r_scangle_it 3.046 r_scbond_it 2.059 r_angle_refined_deg 1.4 r_mcangle_it 1.271 r_mcbond_it 0.831 r_angle_other_deg 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.319 r_dihedral_angle_4_deg 15.642 r_dihedral_angle_3_deg 12.547 r_dihedral_angle_1_deg 5.289 r_scangle_it 3.046 r_scbond_it 2.059 r_angle_refined_deg 1.4 r_mcangle_it 1.271 r_mcbond_it 0.831 r_angle_other_deg 0.814 r_metal_ion_refined 0.337 r_nbd_refined 0.213 r_symmetry_vdw_other 0.204 r_mcbond_other 0.18 r_nbtor_refined 0.177 r_nbd_other 0.176 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.108 r_nbtor_other 0.083 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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 5851 Nucleic Acid Atoms Solvent Atoms 1983 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing