☰ Navigation Tabs
Crystal structure of YdaL, a stand-alone small MutS-related protein from Escherichia coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 1.5M ammonium sulfate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K 2 VAPOR DIFFUSION, HANGING DROP 6 289 1.5M ammonium sulfate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.517 α = 90 b = 34.833 β = 90 c = 40.698 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX225HE 2010-01-31 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 225 mm CCD 2010-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9790 SPring-8 BL41XU 2 SYNCHROTRON SSRF BEAMLINE BL17U 1.5028 SSRF BL17U
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 1,2 2.3 50 100 0.061 0.064 24.3 5.9 6306 6306 1 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) 1,2 2.3 2.38 98.2 0.169 0.242 8.26 5.5 587
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD, MOLECULAR REPLACEMENT THROUGHOUT 2.3 47.76 6306 6306 323 0.22516 0.22516 0.22415 0.2189 0.24358 0.2032 RANDOM 29.485
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] -0.89 0.07 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.297 r_dihedral_angle_4_deg 22.424 r_dihedral_angle_3_deg 17.487 r_dihedral_angle_1_deg 5.877 r_angle_refined_deg 1.367 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.297 r_dihedral_angle_4_deg 22.424 r_dihedral_angle_3_deg 17.487 r_dihedral_angle_1_deg 5.877 r_angle_refined_deg 1.367 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1043 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHENIX model building REFMAC refinement HKL-2000 data reduction SCALA data scaling PHENIX phasing