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AGAO in complex with wc5 (Ru-wire inhibitor, 5-carbon linker)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W6G PDB ENTRY 1W6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 6.0, 800 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK, OVER THREE DAYS. 25 MG OF THE INHIBITOR (WC5) DISSOLVED IN 250 MICROLITRE ETHANOL. 1MICROLITRE OF THIS WAS ADDED TO THE 200MICROLITRE RESERVOIR. GLYCEROL WAS THEN, ADDED IN 2-3% INCREMENTS, TO THE RESERVOIR, WITH THE NEW RESERVOIR SOLUTION SUBSTITUTING THE DROP SOLUTION. THE SOAK SAT FOR 24 HOURS AT 5% GLYCEROL. THE FINAL GLYCEROL CONCENTRATION WAS 30%.
Crystal Properties Matthews coefficient Solvent content 3.06 59.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.885 α = 90 b = 62.944 β = 112.2 c = 92.013 γ = 90
Symmetry Space Group C 1 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 MARRESEARCH OSMIC MIRRORS 2004-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.79 15 99 0.03 24.4 4.2 322625 -3 21.59
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) 1 1.79 1.85 76.8 0.15 4.33 2.58
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 1W6G 1.8 15.02 72905 3847 98.9 0.146 0.145 0.1715 0.165 0.1881 RANDOM 21.96
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] -1.71 0.14 3.04 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.261 r_scangle_it 5.76 r_scbond_it 3.95 r_mcangle_it 2.843 r_mcbond_it 1.744 r_angle_refined_deg 1.505 r_angle_other_deg 0.791 r_symmetry_vdw_other 0.308 r_nbd_other 0.251 r_nbd_refined 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.261 r_scangle_it 5.76 r_scbond_it 3.95 r_mcangle_it 2.843 r_mcbond_it 1.744 r_angle_refined_deg 1.505 r_angle_other_deg 0.791 r_symmetry_vdw_other 0.308 r_nbd_other 0.251 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.184 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.083 r_nbtor_other 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4868 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling