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ADC-7 in complex with boronic acid transition state inhibitor CR167
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 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.79 α = 90 b = 81.045 β = 113.45 c = 105.058 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 1.07820 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 1.804 81.459 99.4 0.059 0.999 15.1 3.8 124952
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 1.804 1.81 99.2 0.662 0.758 2.1 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4U0T 1.804 81.459 118659 6269 99.31 0.18526 0.18284 0.23231 0.2323 RANDOM 32.77
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] 0.35 0.97 -1.67 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.768 r_dihedral_angle_4_deg 21.16 r_dihedral_angle_3_deg 15.061 r_dihedral_angle_1_deg 7.193 r_long_range_B_refined 6.216 r_long_range_B_other 6.207 r_scangle_other 5.106 r_mcangle_other 3.626 r_mcangle_it 3.625 r_scbond_it 3.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.768 r_dihedral_angle_4_deg 21.16 r_dihedral_angle_3_deg 15.061 r_dihedral_angle_1_deg 7.193 r_long_range_B_refined 6.216 r_long_range_B_other 6.207 r_scangle_other 5.106 r_mcangle_other 3.626 r_mcangle_it 3.625 r_scbond_it 3.556 r_scbond_other 3.555 r_mcbond_it 2.89 r_mcbond_other 2.889 r_angle_refined_deg 1.952 r_angle_other_deg 1.08 r_chiral_restr 0.147 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 11104 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building