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Functional domain of InlJ from Listeria monocytogenes includes a cysteine ladder
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 298 2M Ammonium sulfate, 0.1M Na acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.31 62.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.272 α = 90 b = 159.272 β = 90 c = 159.272 γ = 90
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 MAR CCD 165 mm Si [111], horizontally focussing 2006-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.817 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 21.28 99.9 0.112 0.112 17.9 11.2 18505 18486 1 1 49.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 0.391 0.391 5.3 7.1 1809
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1O6V 2.7 21.28 18505 17059 919 97.17 0.18512 0.18152 0.2044 0.25261 0.2564 RANDOM 16.976
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.172 r_dihedral_angle_3_deg 12.189 r_dihedral_angle_1_deg 5.712 r_scangle_it 4.312 r_mcangle_it 3.968 r_dihedral_angle_4_deg 3.287 r_mcbond_it 3.151 r_scbond_it 3.145 r_angle_refined_deg 1.815 r_angle_other_deg 1.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.172 r_dihedral_angle_3_deg 12.189 r_dihedral_angle_1_deg 5.712 r_scangle_it 4.312 r_mcangle_it 3.968 r_dihedral_angle_4_deg 3.287 r_mcbond_it 3.151 r_scbond_it 3.145 r_angle_refined_deg 1.815 r_angle_other_deg 1.733 r_mcbond_other 0.517 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.172 r_symmetry_vdw_other 0.154 r_nbd_other 0.153 r_nbtor_refined 0.142 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.112 r_nbtor_other 0.069 r_chiral_restr 0.062 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3498 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing