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Internalin domain of Listeria monocytogenes InlB: triclinic 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, SITTING DROP 293 SITTING DROP AT 293K WITH 200 NL PROTEIN PLUS 100 NL RESERVOIR SOLUTION CONSISTING OF: 0.1 M LI2SO4, 0.1 M NA-CITRATE PH 5.6, 30% PEG400. THE PROTEIN WAS A COMPLEX CONSISTING OF MET741 AND INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG7ML. CRYSTAL GROWTH TIME WAS SEVERAL MONTHS.
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.66 α = 74.47 b = 70.65 β = 83.13 c = 124.66 γ = 85.65
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 2.6 20 92.1 0.14 10.13 4.96 55139 -3
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 2.6 2.67 74.8 0.7 2.59 3.42
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 2.6 20 52393 2746 92.4 0.194 0.191 0.2067 0.249 0.2581 RANDOM 30.64
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] -0.02 -0.41 -0.01 2.07 -0.38 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.214 r_dihedral_angle_4_deg 15.2 r_dihedral_angle_3_deg 13.333 r_dihedral_angle_1_deg 5.465 r_angle_refined_deg 0.978 r_scangle_it 0.837 r_angle_other_deg 0.812 r_scbond_it 0.484 r_mcangle_it 0.28 r_mcbond_it 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.214 r_dihedral_angle_4_deg 15.2 r_dihedral_angle_3_deg 13.333 r_dihedral_angle_1_deg 5.465 r_angle_refined_deg 0.978 r_scangle_it 0.837 r_angle_other_deg 0.812 r_scbond_it 0.484 r_mcangle_it 0.28 r_mcbond_it 0.141 r_chiral_restr 0.054 r_mcbond_other 0.023 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_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 13226 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing