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Structure of the BtuB:TonB Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NQH PDB ENTRY 1NQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.1 288 30% (v/v) PEG 300, 0.1M sodium acetate , pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 288K, pH 5.10
Crystal Properties Matthews coefficient Solvent content 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.34 α = 90 b = 82.439 β = 90 c = 122.632 γ = 90
Symmetry Space Group P 21 21 21
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 300 mm CCD 2005-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 2.098 40 98.2 0.078 11.9 4.6 44005
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 2.1 2.18 90.5 0.436 2.9
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 (All) 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 1NQH 2.1 40 43953 43953 1191 98.1 0.197 0.197 0.196 0.1996 0.251 0.2523 RANDOM 28.33
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] 0.94 -0.27 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.594 r_dihedral_angle_4_deg 20.607 r_dihedral_angle_3_deg 15.813 r_dihedral_angle_1_deg 7.454 r_scangle_it 4.494 r_scbond_it 3.249 r_angle_refined_deg 2.223 r_mcangle_it 1.97 r_mcbond_it 1.281 r_angle_other_deg 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.594 r_dihedral_angle_4_deg 20.607 r_dihedral_angle_3_deg 15.813 r_dihedral_angle_1_deg 7.454 r_scangle_it 4.494 r_scbond_it 3.249 r_angle_refined_deg 2.223 r_mcangle_it 1.97 r_mcbond_it 1.281 r_angle_other_deg 1.04 r_mcbond_other 0.377 r_symmetry_vdw_other 0.272 r_symmetry_vdw_refined 0.257 r_nbd_other 0.215 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.203 r_nbtor_refined 0.19 r_xyhbond_nbd_other 0.14 r_metal_ion_refined 0.138 r_chiral_restr 0.127 r_nbtor_other 0.098 r_symmetry_hbond_refined 0.073 r_bond_refined_d 0.025 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5194 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 190
Software Software Software Name Purpose MAR345 data collection SERGUI data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement