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X-ray crystal structure of Listeria monocytogenes EGD-e UDP-N-acetylenolpyruvylglucosamine reductase (MurB)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 293 2.2 M Ammonium sulfate, 20% w/v Glycerol, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.55 65.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.21 α = 90 b = 95.21 β = 90 c = 189.895 γ = 120
Symmetry Space Group P 61 2 2
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 225 mm CCD BE 2011-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.69 50 100 0.075 42.7 15.6 14888 14888 -3 55.6
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) 1 2.69 2.74 100 0.37 6.9 14.6
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 1HSK 2.69 50 14082 14082 750 100 0.21566 0.213 0.2149 0.26851 0.2682 RANDOM 49.613
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] -0.12 -0.06 -0.12 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.126 r_dihedral_angle_3_deg 16.373 r_dihedral_angle_4_deg 13.81 r_dihedral_angle_1_deg 4.024 r_angle_refined_deg 2.05 r_chiral_restr 0.123 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.126 r_dihedral_angle_3_deg 16.373 r_dihedral_angle_4_deg 13.81 r_dihedral_angle_1_deg 4.024 r_angle_refined_deg 2.05 r_chiral_restr 0.123 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 2242 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 75
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling