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2.25 Angstrom resolution crystal structure of UDP-N-acetylmuramate--L-alanine ligase (murC) from Yersinia pestis CO92 in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F00 PDB entry 2F00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein 7.4 mg/mL in 10 mM Tris-HCl pH8.3 0.5 M NaCl 5 mM BME, 1 mM ADP, 1 mM MgCl2
Crystallization: The PACT Suite (G7) - 0.2 M Sodium acetate 0.1 M Bis Tris propane pH 7.5 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.2 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.534 α = 90 b = 78.021 β = 90 c = 183.296 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 100 CCD MARMOSAIC 300 mm CCD Be Lenses 2012-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.25 30 99.3 0.093 17.8 6.9 45997 45997 -3 36.8
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 2.25 2.29 98.2 0.554 3.68 6.8 2259
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 (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 2F00 2.25 29.7 43511 43511 2317 99.28 0.18184 0.1795 0.1835 0.22437 0.2269 RANDOM 31.203
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] -1.41 -1.1 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.795 r_dihedral_angle_4_deg 12.677 r_dihedral_angle_3_deg 10.753 r_scangle_it 4.48 r_scbond_it 2.881 r_dihedral_angle_1_deg 2.503 r_mcangle_it 1.691 r_angle_refined_deg 1.589 r_mcbond_it 0.915 r_angle_other_deg 0.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.795 r_dihedral_angle_4_deg 12.677 r_dihedral_angle_3_deg 10.753 r_scangle_it 4.48 r_scbond_it 2.881 r_dihedral_angle_1_deg 2.503 r_mcangle_it 1.691 r_angle_refined_deg 1.589 r_mcbond_it 0.915 r_angle_other_deg 0.867 r_mcbond_other 0.248 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7099 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 54
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling