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Crystal Structure of VanG D-Ala:D-Ser Ligase from Enterococcus faecalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E4E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 0.5M ammonium sulfate, 0.9M lithium sulfate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.32 71.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.07 α = 90 b = 116.07 β = 90 c = 177.228 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r 2009-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 1
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 2.35 33.51 98.5 0.066 12.3 3.7 57000 57000 -3 53.3
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 2.35 2.48 98.6 0.778 1.9 3.8 8252
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 (All) 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 1E4E 2.35 33.5 55248 55248 1747 98.07 0.19026 0.19026 0.1892 0.22412 0.2133 RANDOM 43.033
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] 1.99 1 1.99 -2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.982 r_dihedral_angle_4_deg 23.335 r_dihedral_angle_3_deg 16.392 r_dihedral_angle_1_deg 5.982 r_scangle_it 3.155 r_mcangle_it 2.254 r_scbond_it 1.912 r_angle_refined_deg 1.402 r_mcbond_it 1.216 r_angle_other_deg 0.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.982 r_dihedral_angle_4_deg 23.335 r_dihedral_angle_3_deg 16.392 r_dihedral_angle_1_deg 5.982 r_scangle_it 3.155 r_mcangle_it 2.254 r_scbond_it 1.912 r_angle_refined_deg 1.402 r_mcbond_it 1.216 r_angle_other_deg 0.854 r_mcbond_other 0.177 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 5342 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 99
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling