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Crystal structure of Staphylococcus aureus VRSA-9 D-Ala:D-Ala ligase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I87 PDB ENTRY 2I87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 2M ammonium sulfate, 80mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.04 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.374 α = 90 b = 87.271 β = 90 c = 91.789 γ = 90
Symmetry Space Group P 21 21 21
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 SI (111) CHANNEL-CUT 2010-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97919 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 2.3 43.64 96.2 0.063 16.7 4.5 30788 29619 -3 38.6
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) 2.3 2.42 86 0.369 3.2 3.3 3776
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2I87 2.3 43.64 29558 28076 1482 96.09 0.20398 0.20398 0.20012 0.2017 0.2755 0.2766 RANDOM 27.07
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] -0.83 0.18 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.175 r_dihedral_angle_4_deg 24.404 r_dihedral_angle_3_deg 16.967 r_dihedral_angle_1_deg 6.327 r_scangle_it 3.171 r_scbond_it 1.862 r_angle_refined_deg 1.358 r_mcangle_it 1.351 r_angle_other_deg 0.863 r_mcbond_it 0.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.175 r_dihedral_angle_4_deg 24.404 r_dihedral_angle_3_deg 16.967 r_dihedral_angle_1_deg 6.327 r_scangle_it 3.171 r_scbond_it 1.862 r_angle_refined_deg 1.358 r_mcangle_it 1.351 r_angle_other_deg 0.863 r_mcbond_it 0.714 r_mcbond_other 0.114 r_chiral_restr 0.076 r_bond_refined_d 0.011 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 5283 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 73
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling