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Crystal structure of prophage tail protein gp18 (NP_465809.1) from Listeria monocytogenes EGD-e at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.65 293 NANODROP, 10.0% PEG 1000, 0.20M Lithium sulfate, 0.1M Phosphate-citrate pH 4.65, VAPOR DIFFUSION, SITTING DROP, temperature 293K 2 VAPOR DIFFUSION, SITTING DROP 4.36 293 NANODROP, 11.50% PEG 6000, 0.1M Citric acid pH 4.36, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.575 α = 90 b = 135.575 β = 90 c = 59.172 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 100 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-11-15 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-12-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97975, 0.97956 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.7 28.689 100 0.085 0.085 9.8 2.9 44621 20.937
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.7 1.74 100 0.498 0.498 1.8 2.9 3320
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.7 28.689 44619 2298 99.98 0.189 0.187 0.1903 0.223 0.2228 RANDOM 24.197
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] -0.47 -0.23 -0.47 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.882 r_dihedral_angle_4_deg 18.023 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_1_deg 6.139 r_scangle_it 5.988 r_scbond_it 4.405 r_mcangle_it 2.866 r_mcbond_it 1.979 r_angle_refined_deg 1.394 r_angle_other_deg 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.882 r_dihedral_angle_4_deg 18.023 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_1_deg 6.139 r_scangle_it 5.988 r_scbond_it 4.405 r_mcangle_it 2.866 r_mcbond_it 1.979 r_angle_refined_deg 1.394 r_angle_other_deg 0.88 r_mcbond_other 0.518 r_symmetry_vdw_other 0.258 r_nbd_refined 0.202 r_nbd_other 0.192 r_nbtor_refined 0.182 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.09 r_nbtor_other 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2675 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing autoSHARP phasing