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Crystal structure of Burkholderia AP3 phage endolysin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M SPG pH 7.0, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.615 α = 90 b = 154.615 β = 90 c = 125.823 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS PILATUS3 S 6M 2016-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.91841 PETRA III, DESY P11
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 1.72 26.72 100 0.126 0.993 11.1 9.1 61070
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 1.72 1.75 100 0.684 0.791 3.3 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.72 26.72 58039 3029 99.96 0.2097 0.20837 0.23528 0.266 RANDOM 29.162
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] 0.17 0.08 0.17 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.544 r_dihedral_angle_4_deg 21.679 r_dihedral_angle_3_deg 12.902 r_long_range_B_refined 5.294 r_long_range_B_other 5.294 r_dihedral_angle_1_deg 5.125 r_scangle_other 4.106 r_mcangle_other 2.782 r_mcangle_it 2.78 r_scbond_it 2.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.544 r_dihedral_angle_4_deg 21.679 r_dihedral_angle_3_deg 12.902 r_long_range_B_refined 5.294 r_long_range_B_other 5.294 r_dihedral_angle_1_deg 5.125 r_scangle_other 4.106 r_mcangle_other 2.782 r_mcangle_it 2.78 r_scbond_it 2.602 r_scbond_other 2.602 r_mcbond_it 1.898 r_mcbond_other 1.888 r_angle_refined_deg 1.403 r_angle_other_deg 1.293 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.006 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 3970 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing