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Crystal structure of F47Y variant of TenA (HP1287) from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.1M Tris, 1.1M lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.728 α = 90 b = 148.728 β = 90 c = 233.566 γ = 90
Symmetry Space Group I 41 2 2
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 QUANTUM 315r 2009-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9794 ESRF ID14-4
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 2.4 125 99.7 0.153 8.6 9.9 51200 51200
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 2.4 2.53 100 0.46 3.7 10.2 7412
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 2RD3 2.4 78 51200 50181 2541 97.74 0.21831 0.21771 0.2128 0.22957 0.2266 RANDOM 20.875
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 0.38 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.632 r_dihedral_angle_3_deg 19.346 r_dihedral_angle_4_deg 16.989 r_dihedral_angle_1_deg 4.556 r_scangle_it 2.119 r_scbond_it 1.299 r_angle_refined_deg 1.245 r_mcangle_it 0.853 r_mcbond_it 0.417 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.632 r_dihedral_angle_3_deg 19.346 r_dihedral_angle_4_deg 16.989 r_dihedral_angle_1_deg 4.556 r_scangle_it 2.119 r_scbond_it 1.299 r_angle_refined_deg 1.245 r_mcangle_it 0.853 r_mcbond_it 0.417 r_chiral_restr 0.115 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3553 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling