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InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant 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 VAPOR DIFFUSION, SITTING DROP 293 SITTING DROP VAPOUR DIFFUSION AT 293K WITH 1 UL PROTEIN (3.8 MG/ML IN 50 MM HEPES, PH 7.0, 100 MM NACL) PLUS 0.5 UL RESERVOIR (17% PEG1000MME, 90 MM NA-CITRATE).
Crystal Properties Matthews coefficient Solvent content 2.14 0.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.7 α = 102.99 b = 57.45 β = 90.21 c = 64.3 γ = 93.56
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 RIGAKU SATURN 944PLUS VARIMAX HF 2009-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.03 20 96.8 0.12 12.65 5.1 33525 -3 20.09
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 2.03 2.09 68.5 0.41 4.02 3.7
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 2.03 38.63 31849 1677 100 0.19729 0.19423 0.2077 0.2567 0.2667 RANDOM 12.299
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] -0.38 0.24 0.15 0.93 -0.01 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.146 r_dihedral_angle_4_deg 19.117 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_1_deg 6.969 r_scangle_it 4.098 r_scbond_it 2.543 r_angle_refined_deg 1.799 r_mcangle_it 1.46 r_angle_other_deg 1.081 r_mcbond_it 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.146 r_dihedral_angle_4_deg 19.117 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_1_deg 6.969 r_scangle_it 4.098 r_scbond_it 2.543 r_angle_refined_deg 1.799 r_mcangle_it 1.46 r_angle_other_deg 1.081 r_mcbond_it 0.85 r_mcbond_other 0.274 r_chiral_restr 0.109 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 4546 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing