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New azaborine compounds bind to the T4 lysozyme L99A cavity - Benzene as control
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 2.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60 α = 90 b = 60 β = 90 c = 95.65 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 51.96 100 0.067 34.3 15.3 57244 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 0.267 10.7 10.4 2834
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 3DMV 1.25 51.96 52835 2832 99.86 0.16768 0.16641 0.1917 0.2115 RANDOM 15.664
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.709 r_dihedral_angle_4_deg 16.73 r_dihedral_angle_3_deg 12.313 r_dihedral_angle_1_deg 4.92 r_sphericity_free 3.218 r_scangle_it 2.886 r_sphericity_bonded 2.723 r_scbond_it 2.312 r_rigid_bond_restr 1.85 r_mcangle_it 1.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.709 r_dihedral_angle_4_deg 16.73 r_dihedral_angle_3_deg 12.313 r_dihedral_angle_1_deg 4.92 r_sphericity_free 3.218 r_scangle_it 2.886 r_sphericity_bonded 2.723 r_scbond_it 2.312 r_rigid_bond_restr 1.85 r_mcangle_it 1.399 r_angle_refined_deg 1.173 r_mcbond_it 0.92 r_nbtor_refined 0.315 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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_refined 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 1428 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 27
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling