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Crystal structure of MOX-1 complexed with a boronic acid transition state inhibitor S02030
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 PEG 8000, 100 mM sodium cacodylate buffer (pH 6.5), 0.2 M zinc acetate
Crystal Properties Matthews coefficient Solvent content 2.23 44.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.64 α = 90 b = 59.2 β = 102.03 c = 62.89 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 PIXEL DECTRIS PILATUS3 S 6M 2016-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.13 61.51 99.9 10.8 3.2 20024
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.18 100
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 3W8K 2.13 42.69 19050 957 99.84 0.15979 0.15753 0.1701 0.2048 0.2136 RANDOM 23.931
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] 0.11 1.41 -1.85 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.804 r_dihedral_angle_4_deg 17.721 r_dihedral_angle_3_deg 12.629 r_dihedral_angle_1_deg 6.768 r_long_range_B_refined 5.149 r_long_range_B_other 5.119 r_scangle_other 3.683 r_scbond_it 2.355 r_scbond_other 2.355 r_mcangle_it 2.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.804 r_dihedral_angle_4_deg 17.721 r_dihedral_angle_3_deg 12.629 r_dihedral_angle_1_deg 6.768 r_long_range_B_refined 5.149 r_long_range_B_other 5.119 r_scangle_other 3.683 r_scbond_it 2.355 r_scbond_other 2.355 r_mcangle_it 2.276 r_mcangle_other 2.275 r_mcbond_it 1.533 r_mcbond_other 1.511 r_angle_refined_deg 1.279 r_angle_other_deg 0.95 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 2631 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing