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Structure of the Yersinia enterocolitica Type III Secretion Translocator Chaperone SycD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FO7 PDB ENTRY 2FO7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 277 0.1M TRI-SODIUM CITRATE, 20% PEG 4000, 20% 2-PROPANOL AT 4 DEGREES CELSIUS
Crystal Properties Matthews coefficient Solvent content 2.5 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.247 α = 90 b = 32.979 β = 122.34 c = 96.731 γ = 90
Symmetry Space Group C 1 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 ADSC CCD 2007-02-15 M SINGLE WAVELENGTH 2 1 x-ray M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1 2 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) 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 1.95 45.3 99.6 0.09 0.1 13.1 4 21282 3 22.1
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) 1 1.95 2.05 99.8 0.31 0.41 3.8 3.6
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 2FO7 1.95 45.31 20217 1065 100 0.178 0.175 0.1764 0.227 0.2285 RANDOM 19.93
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] -0.91 -0.13 0.2 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.967 r_dihedral_angle_4_deg 11.81 r_dihedral_angle_3_deg 11.743 r_dihedral_angle_1_deg 4.39 r_scangle_it 3.542 r_mcangle_it 2.998 r_scbond_it 2.439 r_mcbond_it 2.014 r_angle_refined_deg 1.443 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.967 r_dihedral_angle_4_deg 11.81 r_dihedral_angle_3_deg 11.743 r_dihedral_angle_1_deg 4.39 r_scangle_it 3.542 r_mcangle_it 2.998 r_scbond_it 2.439 r_mcbond_it 2.014 r_angle_refined_deg 1.443 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.273 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 2205 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing