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ADC-7 in complex with boronic acid transition state inhibitor S03043
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 2.18 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.012 α = 90 b = 81.3 β = 112.7 c = 106.438 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 RAYONIX MX-300 2014-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.878 82.11 99.8 0.067 0.998 13.5 4.2 113977
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 1.878 1.885 99.8 0.624 0.732 2.2 4.2
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 1.88 50 108274 5673 99.68 0.20456 0.20182 0.25619 0.2684 RANDOM 35.27
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] 0.41 0.91 -1.92 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.124 r_dihedral_angle_3_deg 15.201 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_1_deg 7.261 r_long_range_B_refined 6.266 r_long_range_B_other 6.251 r_scangle_other 4.838 r_mcangle_it 4.252 r_mcangle_other 4.251 r_scbond_it 3.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.124 r_dihedral_angle_3_deg 15.201 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_1_deg 7.261 r_long_range_B_refined 6.266 r_long_range_B_other 6.251 r_scangle_other 4.838 r_mcangle_it 4.252 r_mcangle_other 4.251 r_scbond_it 3.438 r_scbond_other 3.438 r_mcbond_it 3.233 r_mcbond_other 3.23 r_angle_refined_deg 1.896 r_angle_other_deg 1.101 r_chiral_restr 0.117 r_bond_refined_d 0.018 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 10977 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building