☰ Navigation Tabs
Crystal Structure of Internalin C from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H6T truncated model of Internalin B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 magnesium sulfate and MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.82 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.327 α = 90 b = 177.802 β = 90 c = 42.222 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 2002-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6
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 30 87.7 0.091 0.091 16.3 3.6 28367 24878 26.9
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) 2 77.2 0.484 0.484 2.2 3.6 21899
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT truncated model of Internalin B 2.05 19.76 27434 23591 1255 30 0.228 0.2023 0.20016 0.2128 0.24256 RANDOM 25.781
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] -0.61 1.7 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.428 r_scangle_it 4.552 r_dihedral_angle_1_deg 4.403 r_scbond_it 2.694 r_angle_refined_deg 1.644 r_mcangle_it 1.603 r_mcbond_it 0.82 r_angle_other_deg 0.797 r_symmetry_hbond_refined 0.347 r_nbd_refined 0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.428 r_scangle_it 4.552 r_dihedral_angle_1_deg 4.403 r_scbond_it 2.694 r_angle_refined_deg 1.644 r_mcangle_it 1.603 r_mcbond_it 0.82 r_angle_other_deg 0.797 r_symmetry_hbond_refined 0.347 r_nbd_refined 0.245 r_nbd_other 0.222 r_xyhbond_nbd_refined 0.212 r_symmetry_vdw_other 0.201 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_other 0.117 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2080 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing