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E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES pH7.5, 25% PEG4000, 0.3 M Lithium Sulfate, 0.1 M Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.27 α = 109.3 b = 68.07 β = 92.98 c = 87.13 γ = 117.23
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 PIXEL DECTRIS PILATUS 6M 2013-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.987 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.33 50 96.9 11.42 3.18 49021
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 2.33 49.04 46561 2451 97.08 0.20479 0.20229 0.2073 0.25265 0.2537 RANDOM 32.394
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] 0.55 0.47 0.52 0.81 0.3 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.855 r_dihedral_angle_4_deg 14.907 r_dihedral_angle_3_deg 14.281 r_long_range_B_refined 6.264 r_long_range_B_other 6.264 r_dihedral_angle_1_deg 5.732 r_scangle_other 5.29 r_mcangle_it 4.271 r_mcangle_other 4.271 r_scbond_other 3.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.855 r_dihedral_angle_4_deg 14.907 r_dihedral_angle_3_deg 14.281 r_long_range_B_refined 6.264 r_long_range_B_other 6.264 r_dihedral_angle_1_deg 5.732 r_scangle_other 5.29 r_mcangle_it 4.271 r_mcangle_other 4.271 r_scbond_other 3.938 r_scbond_it 3.937 r_mcbond_it 3.116 r_mcbond_other 3.113 r_angle_refined_deg 1.454 r_angle_other_deg 0.851 r_chiral_restr 0.08 r_gen_planes_refined 0.015 r_bond_refined_d 0.014 r_gen_planes_other 0.011 r_bond_other_d 0.01 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8337 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement