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Crystal structure of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.9 281 16.7% PEG6000, NaF 135mM, LiCl 296mM, NaAC 100mM, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.36 47.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.41 α = 90.13 b = 67.573 β = 68.85 c = 77.998 γ = 72.29
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 ADSC QUANTUM 210 2008-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9536 Australian Synchrotron MX1
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 1.45 30.25 91.4 0.057 0.057 18.8 3.9 190869 2 2 9.84
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 1.45 1.53 71.9 0.147 0.147 8.4 3.9 21900
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 1yxc 1.45 30.25 181258 9610 100 0.13371 0.13229 0.1419 0.16084 0.1674 RANDOM 8.073
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 -0.08 -0.34 -0.38 -0.13 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_3_deg 11.27 r_dihedral_angle_4_deg 11.077 r_dihedral_angle_1_deg 9.927 r_sphericity_free 2.812 r_scangle_it 2.63 r_scbond_it 1.762 r_sphericity_bonded 1.329 r_angle_refined_deg 1.271 r_mcangle_it 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_3_deg 11.27 r_dihedral_angle_4_deg 11.077 r_dihedral_angle_1_deg 9.927 r_sphericity_free 2.812 r_scangle_it 2.63 r_scbond_it 1.762 r_sphericity_bonded 1.329 r_angle_refined_deg 1.271 r_mcangle_it 1.08 r_angle_other_deg 0.887 r_rigid_bond_restr 0.772 r_mcbond_it 0.767 r_symmetry_vdw_refined 0.255 r_mcbond_other 0.244 r_nbd_refined 0.216 r_symmetry_vdw_other 0.197 r_nbd_other 0.179 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.117 r_symmetry_hbond_refined 0.097 r_nbtor_other 0.087 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9024 Nucleic Acid Atoms Solvent Atoms 1795 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASES phasing