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Internalin domain of Listeria monocytogenes InlB: rhombohedral crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H6T PDB ENTRY 1H6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 SITTING VAPOR DIFFUSION AT 293 K. 200 NL PROTEIN PLUS 100 NL OF RESERVOIR SOLUTION CONSISTING OF 0.1 M NACL, 0.1 M CHES PH 9.5, 40% PEG300. THE PROTEIN WAS ACTUALLY A COMPLEX OF MET741 WITH INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG/ML. CRYSTAL GROWTH TIME: SEVERAL WEEKS TO MONTHS.
Crystal Properties Matthews coefficient Solvent content 2.97 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.9 α = 90 b = 185.9 β = 90 c = 115.07 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 MARRESEARCH 2006-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.8 20 99.3 0.16 10.98 6.96 18763 -3 45.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 100 0.91 2.58 7.08
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1H6T 2.8 19.822 18762 941 99.692 0.205 0.2033 0.2128 0.2378 0.2475 RANDOM 40.35
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] 2.278 1.139 2.278 -3.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.594 r_dihedral_angle_3_deg 14.609 r_dihedral_angle_4_deg 13.99 r_dihedral_angle_1_deg 5.979 r_scangle_it 1.11 r_angle_refined_deg 1.072 r_angle_other_deg 0.815 r_scbond_it 0.771 r_mcangle_it 0.387 r_mcbond_it 0.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.594 r_dihedral_angle_3_deg 14.609 r_dihedral_angle_4_deg 13.99 r_dihedral_angle_1_deg 5.979 r_scangle_it 1.11 r_angle_refined_deg 1.072 r_angle_other_deg 0.815 r_scbond_it 0.771 r_mcangle_it 0.387 r_mcbond_it 0.334 r_symmetry_vdw_other 0.212 r_nbd_refined 0.195 r_nbd_other 0.185 r_nbtor_refined 0.168 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_refined 0.125 r_nbtor_other 0.082 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4436 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing