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Crystal structure of the human-specific toxin intermedilysin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 PEG 8000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.68 66.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.45 α = 90 b = 173.64 β = 90 c = 105.11 γ = 90
Symmetry Space Group P 21 21 2
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 4 2002-07-14 M SINGLE WAVELENGTH 2 1 100 IMAGE PLATE MARRESEARCH mirrors 2002-04-23
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C 2 ROTATING ANODE RIGAKU 1.54
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 2.5 30 99.2 0.047 0.047 37.7 6 50420 50420 81.7
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 2.5 2.59 97.6 0.368 0.368 4.5 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MIR THROUGHOUT 2.6 30 50420 47850 2570 99.83 0.265 0.23233 0.22901 0.2385 0.2951 0.3069 RANDOM 35.356
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] 12.99 -9.54 -3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.113 r_scangle_it 2.943 r_scbond_it 1.844 r_angle_refined_deg 1.582 r_mcangle_it 1.301 r_angle_other_deg 0.905 r_mcbond_it 0.721 r_nbd_other 0.251 r_symmetry_vdw_other 0.251 r_nbd_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.113 r_scangle_it 2.943 r_scbond_it 1.844 r_angle_refined_deg 1.582 r_mcangle_it 1.301 r_angle_other_deg 0.905 r_mcbond_it 0.721 r_nbd_other 0.251 r_symmetry_vdw_other 0.251 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.227 r_xyhbond_nbd_refined 0.19 r_symmetry_vdw_refined 0.134 r_nbtor_other 0.091 r_chiral_restr 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7356 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing