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Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abcessus, bound to ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DXL PDB ENTRY 4DXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 290 Internal tracking number 231560F1, CSHT screen condition F1: 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate, pH 4.6, 30% PEG2000 MME, MyabA.00725.a.A1 PW30213 at 29.3 mg/mL in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 2 mM ATP, 2 mM EBSI1799, cryoprotectant: Al's oil, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.06 40.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.45 α = 90 b = 53.36 β = 90 c = 109.11 γ = 90
Symmetry Space Group P 21 2 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 RIGAKU SATURN 944+ 2012-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.541780
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 1.75 42.738 95.7 0.047 31.98 9.2 26899 -3 20.012
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 1.75 1.8 84.2 0.143 10.8 5.85
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 PDB ENTRY 4DXL 1.75 42.738 26898 1370 95.6 0.169 0.166 0.1727 0.213 0.217 RANDOM 14.343
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] -0.04 -0.3 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.926 r_dihedral_angle_4_deg 15.52 r_dihedral_angle_3_deg 11.958 r_dihedral_angle_1_deg 7.133 r_angle_refined_deg 1.535 r_angle_other_deg 0.864 r_chiral_restr 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.926 r_dihedral_angle_4_deg 15.52 r_dihedral_angle_3_deg 11.958 r_dihedral_angle_1_deg 7.133 r_angle_refined_deg 1.535 r_angle_other_deg 0.864 r_chiral_restr 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2134 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 31
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing