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Crystal structure of Treponema denticola PurE bound to AIR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native coordinate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 14-16% (W/V) PEG 1000, 0.1 M MAGNESIUM CHLORIDE, 0.1 M IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.39 α = 90 b = 155.13 β = 90 c = 88.14 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 111 IMAGE PLATE RIGAKU RAXIS IV 2006-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.82 37.1 98.6 0.064 20 6.4 51257 51257
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.87 92.3 0.865 2.2 5.1 3520
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Native coordinate 1.82 37.1 48510 48510 2607 98.34 0.18985 0.18816 0.22155 0.2002 RANDOM 28.749
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] -0.84 2.22 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.951 r_dihedral_angle_3_deg 14.381 r_dihedral_angle_4_deg 12.906 r_dihedral_angle_1_deg 5.792 r_scangle_it 3.362 r_scbond_it 2.183 r_angle_refined_deg 1.674 r_mcangle_it 1.212 r_angle_other_deg 0.98 r_mcbond_it 0.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.951 r_dihedral_angle_3_deg 14.381 r_dihedral_angle_4_deg 12.906 r_dihedral_angle_1_deg 5.792 r_scangle_it 3.362 r_scbond_it 2.183 r_angle_refined_deg 1.674 r_mcangle_it 1.212 r_angle_other_deg 0.98 r_mcbond_it 0.731 r_mcbond_other 0.216 r_chiral_restr 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4703 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 76
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling