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New azaborine compounds bind to the T4 lysozyme L99A cavity - 1,2-dihydro-1,2-azaborine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DMV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 277 2.0-2.2M K/Na phosphase, 50mM BME, 50mM HED (vapor-diffusion for complex preparation), pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.904 α = 90 b = 59.904 β = 90 c = 95.443 γ = 120
Symmetry Space Group P 32 2 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 ADSC QUANTUM 315 Si(220) 2009-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9791 ALS 5.0.3
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 1.25 45.58 99.9 0.071 33.6 15.5 55239 5
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) 1.25 1.27 100 0.269 9.1 10.5 2732
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 3DMV 1.25 45.58 52369 2799 99.65 0.16747 0.16642 0.1647 0.18721 0.1854 RANDOM 15.635
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] 0.09 0.05 0.09 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.233 r_dihedral_angle_3_deg 12.721 r_dihedral_angle_4_deg 9.815 r_dihedral_angle_1_deg 4.92 r_sphericity_free 3.267 r_scangle_it 3.008 r_sphericity_bonded 2.877 r_scbond_it 2.049 r_mcangle_it 1.446 r_rigid_bond_restr 1.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.233 r_dihedral_angle_3_deg 12.721 r_dihedral_angle_4_deg 9.815 r_dihedral_angle_1_deg 4.92 r_sphericity_free 3.267 r_scangle_it 3.008 r_sphericity_bonded 2.877 r_scbond_it 2.049 r_mcangle_it 1.446 r_rigid_bond_restr 1.216 r_angle_refined_deg 1.172 r_mcbond_it 0.826 r_nbtor_refined 0.306 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.174 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_metal_ion_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1403 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 34
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling