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The crystal structure of the complex of the C-terminal domain of Helicobacter pylori MotB (residues 125-256) with N-acetylmuramic acid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 100 mM Tris/HCl, 16-18% PEG 3350, 200 mM sodium tartrate, 10 mM N-acetylmuramic acid, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.781 α = 90 b = 110.058 β = 104.58 c = 113.664 γ = 90
Symmetry Space Group P 1 21 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 2007-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9 SLS X06SA
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 2.3 109.76 96 0.099 7 103524
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 2.3 2.42 98 0.316 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.3 15 103503 5187 96.07 0.22 0.217 0.2237 0.289 0.295 RANDOM 18.046
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] -1.63 0.22 0.17 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.056 r_dihedral_angle_4_deg 16.41 r_dihedral_angle_3_deg 15.952 r_scangle_it 6.461 r_dihedral_angle_1_deg 6.217 r_scbond_it 4.87 r_mcangle_it 4.246 r_mcbond_it 3.621 r_angle_refined_deg 1.662 r_angle_other_deg 1.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.056 r_dihedral_angle_4_deg 16.41 r_dihedral_angle_3_deg 15.952 r_scangle_it 6.461 r_dihedral_angle_1_deg 6.217 r_scbond_it 4.87 r_mcangle_it 4.246 r_mcbond_it 3.621 r_angle_refined_deg 1.662 r_angle_other_deg 1.092 r_mcbond_other 1.054 r_symmetry_vdw_refined 0.238 r_symmetry_hbond_refined 0.22 r_symmetry_vdw_other 0.217 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.196 r_nbd_other 0.189 r_nbtor_refined 0.18 r_nbtor_other 0.089 r_chiral_restr 0.082 r_xyhbond_nbd_other 0.033 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17110 Nucleic Acid Atoms Solvent Atoms 1274 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing