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The Crystal Structure of Pyocin L1 at 2.09 Angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MSA PDB ENTRY 1MSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% v/v ethylene glycol, 10% w/v PEG 8000, 0.03 M CaCl2, 0.03 M MgCl2, 0.1 M Tris/Bicine, , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.41 α = 90 b = 158.4 β = 90 c = 147.67 γ = 90
Symmetry Space Group C 2 2 21
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 PSI PILATUS 6M 2012-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97620 Diamond I04-1
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 2.09 36.39 99 0.072 14.3 4.8 37131 2 2
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 2.09 2.14 99.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1MSA 2.09 36.39 2.1 35246 1858 98.67 0.18027 0.18027 0.17808 0.1874 0.2215 0.2273 RANDOM 40.172
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] -2.74 1.63 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.687 r_dihedral_angle_4_deg 23.368 r_dihedral_angle_3_deg 15.626 r_dihedral_angle_1_deg 8.383 r_long_range_B_refined 7.798 r_long_range_B_other 7.639 r_scangle_other 3.798 r_mcangle_other 3.295 r_mcangle_it 3.294 r_scbond_it 2.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.687 r_dihedral_angle_4_deg 23.368 r_dihedral_angle_3_deg 15.626 r_dihedral_angle_1_deg 8.383 r_long_range_B_refined 7.798 r_long_range_B_other 7.639 r_scangle_other 3.798 r_mcangle_other 3.295 r_mcangle_it 3.294 r_scbond_it 2.461 r_scbond_other 2.46 r_mcbond_it 2.173 r_mcbond_other 2.163 r_angle_refined_deg 1.863 r_angle_other_deg 0.87 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 3978 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 171
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement xia2 data reduction Aimless data scaling