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ADC-7 in complex with boronic acid transition state inhibitor S06017
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 ADC-7 (3mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine
Crystal Properties Matthews coefficient Solvent content 2.12 42.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.665 α = 90 b = 80.896 β = 113.36 c = 105.338 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 CCD MARMOSAIC 300 mm CCD 2013-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07821 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.931 81.397 97.4 0.078 0.998 10.8 3.8 99952
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.931 1.938 95.9 0.632 0.709 2.1 3.9
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 4U0T 1.931 81.397 94942 4987 97.33 0.18914 0.18608 0.1949 0.24714 0.2497 RANDOM 35.98
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] 0.42 0.97 -1.2 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.12 r_dihedral_angle_4_deg 22.277 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_1_deg 6.997 r_long_range_B_refined 6.07 r_long_range_B_other 6.066 r_scangle_other 5.02 r_mcangle_it 3.841 r_mcangle_other 3.841 r_scbond_it 3.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.12 r_dihedral_angle_4_deg 22.277 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_1_deg 6.997 r_long_range_B_refined 6.07 r_long_range_B_other 6.066 r_scangle_other 5.02 r_mcangle_it 3.841 r_mcangle_other 3.841 r_scbond_it 3.496 r_scbond_other 3.496 r_mcbond_it 2.908 r_mcbond_other 2.907 r_angle_refined_deg 1.864 r_angle_other_deg 1.112 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11033 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building