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Listeria monocytogenes InlB (internalin B) residues 36-392
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 20 DEG C IN HANGING OR SITTING-DROPS WITH 1.5 UL PROTEIN (5 MG/ML) PLUS 1.5 UL RESERVOIR (0.1 M MES, PH 5.5, 14 % MPD) MICROSEEDED FROM A SIMILAR CONDITION (0.1 M MES PH 6.0, 6.5 % PEG6000 AND 5 MM ZNCL2).
Crystal Properties Matthews coefficient Solvent content 6.16 80
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.4 α = 90 b = 126.4 β = 90 c = 107.86 γ = 120
Symmetry Space Group P 32 2 1
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 MARMOSAIC 225 mm CCD 2009-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12
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 3.2 15 98.7 0.13 18.3 14.7 16581 -3 86
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 3.2 3.28 100 0.55 2.9
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 3.2 14.97 15752 829 100 0.19847 0.19713 0.199 0.22475 0.232 RANDOM 73.16
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] 4.69 2.35 4.69 -7.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.273 r_dihedral_angle_3_deg 19.934 r_dihedral_angle_4_deg 10.471 r_dihedral_angle_1_deg 8.955 r_scangle_it 3.514 r_angle_refined_deg 2.037 r_scbond_it 1.973 r_mcangle_it 1.242 r_angle_other_deg 1.134 r_mcbond_it 0.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.273 r_dihedral_angle_3_deg 19.934 r_dihedral_angle_4_deg 10.471 r_dihedral_angle_1_deg 8.955 r_scangle_it 3.514 r_angle_refined_deg 2.037 r_scbond_it 1.973 r_mcangle_it 1.242 r_angle_other_deg 1.134 r_mcbond_it 0.631 r_mcbond_other 0.101 r_chiral_restr 0.1 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d 0.005 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 2271 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing