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DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain
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 9.5 293 293 K. PROTEIN (6.7 MG/ML) PLUS RESERVOIR = 2 PLUS 1. RESERVOIR SOLUTION IS 44-52% PEG2000, 0.1 M CHES PH=9,5, 0.2M NACL., PH 9.5
Crystal Properties Matthews coefficient Solvent content 2.93 57.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.99 α = 90 b = 186.99 β = 90 c = 115.071 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 ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.24 50 99.9 0.12 10.5 7.3 37017 -3 37.8
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 2.24 2.36 99.7 0.88 2 6.9
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 2.24 46.88 35166 1849 99.9 0.201 0.199 0.2077 0.239 0.2396 RANDOM 31.45
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] -1.09 -0.55 -1.09 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.12 r_dihedral_angle_4_deg 23.839 r_dihedral_angle_3_deg 16.593 r_dihedral_angle_1_deg 6.952 r_scangle_it 3.233 r_scbond_it 2.165 r_angle_refined_deg 1.909 r_angle_other_deg 1.259 r_mcangle_it 1.12 r_mcbond_it 0.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.12 r_dihedral_angle_4_deg 23.839 r_dihedral_angle_3_deg 16.593 r_dihedral_angle_1_deg 6.952 r_scangle_it 3.233 r_scbond_it 2.165 r_angle_refined_deg 1.909 r_angle_other_deg 1.259 r_mcangle_it 1.12 r_mcbond_it 0.682 r_mcbond_other 0.258 r_chiral_restr 0.13 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 4512 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing