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Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abcessus, bound to CMP and SO4
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 4.5 290 Internal tracking number 230821D4, JCSG screen condition D4: 30% PEG8000, acetate, pH 4.5, 200 mM lithium sulfate, 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 CDP, 2 mM ATP, 2 mM meso-erythritol, cryoprotectant: 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.07 40.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.44 α = 90 b = 109.93 β = 90 c = 53.1 γ = 90
Symmetry Space Group P 21 21 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 RIGAKU SATURN 944+ 2012-03-29 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 50 99.7 0.062 30.2 9.25 28202 28123 -3 19.352
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 97.4 0.454 2.3 2.54
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 50 28123 1424 99.71 0.161 0.159 0.1674 0.204 0.211 RANDOM 13.579
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] 0.13 0.14 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.134 r_dihedral_angle_4_deg 20.484 r_dihedral_angle_3_deg 11.427 r_dihedral_angle_1_deg 6.68 r_angle_refined_deg 1.53 r_angle_other_deg 0.898 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.134 r_dihedral_angle_4_deg 20.484 r_dihedral_angle_3_deg 11.427 r_dihedral_angle_1_deg 6.68 r_angle_refined_deg 1.53 r_angle_other_deg 0.898 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2135 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 26
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing