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ADC-7 in complex with boronic acid transition state inhibitor CR161
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 2.23 44.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.268 α = 90 b = 81.47 β = 112.5 c = 105.908 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 2013-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07820 APS 21-ID-D
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 2.09 97.845 99.3 0.084 11.5 3.7 82578
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 2.09 2.1 99.8 0.666 2 3.7
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 2.09 97.84 78433 4124 99.3 0.218 0.214 0.2187 0.286 0.2862 RANDOM 36.91
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] 0.02 1.04 -2 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.728 r_dihedral_angle_4_deg 19.8 r_dihedral_angle_3_deg 16.084 r_dihedral_angle_1_deg 7.241 r_long_range_B_refined 6.188 r_long_range_B_other 6.172 r_scangle_other 4.424 r_mcangle_it 4.214 r_mcangle_other 4.213 r_scbond_it 2.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.728 r_dihedral_angle_4_deg 19.8 r_dihedral_angle_3_deg 16.084 r_dihedral_angle_1_deg 7.241 r_long_range_B_refined 6.188 r_long_range_B_other 6.172 r_scangle_other 4.424 r_mcangle_it 4.214 r_mcangle_other 4.213 r_scbond_it 2.942 r_scbond_other 2.935 r_mcbond_it 2.923 r_mcbond_other 2.922 r_angle_refined_deg 1.79 r_angle_other_deg 1.081 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 10785 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building