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Crystal structure of E. coli YgjD-YeaZ heterodimer in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 30% PEG4000, 0.3M Lithium Sulfate, 0.1 M Sodium Acetate and 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.62 α = 109.38 b = 68.48 β = 92.66 c = 87.07 γ = 117.66
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2012-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9801 SOLEIL PROXIMA 1
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 2.25 49.38 97.9 0.121 11 3.97 55653
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 2.25 2.33 95.69 0.57 0.483 2.46
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2IVP 2.33 49.38 52870 2783 97.92 0.20479 0.20229 0.1727 0.25265 0.2206 RANDOM 35.999
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] -0.22 -0.15 -0.05 0.08 0.53 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.596 r_dihedral_angle_4_deg 18.838 r_dihedral_angle_3_deg 12.955 r_dihedral_angle_1_deg 6.016 r_long_range_B_refined 5.215 r_long_range_B_other 5.167 r_scangle_other 4.031 r_mcangle_it 2.784 r_mcangle_other 2.784 r_scbond_it 2.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.596 r_dihedral_angle_4_deg 18.838 r_dihedral_angle_3_deg 12.955 r_dihedral_angle_1_deg 6.016 r_long_range_B_refined 5.215 r_long_range_B_other 5.167 r_scangle_other 4.031 r_mcangle_it 2.784 r_mcangle_other 2.784 r_scbond_it 2.727 r_scbond_other 2.727 r_mcbond_it 1.918 r_mcbond_other 1.901 r_angle_refined_deg 1.662 r_angle_other_deg 0.777 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_gen_planes_other 0.009 r_bond_other_d 0.008 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 8410 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building MOLREP phasing