☰ Navigation Tabs
Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abscessus, bound to CMP and ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PYG PDB ENTRY 3PYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 290 Internal tracking number 230819a2, INDEX screen condition A2: 2 M ammonium sulfate, 0.1 M acetate, pH 4.5, 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: Al's oil, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.59 α = 90 b = 110.09 β = 90 c = 53.29 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+ 2012-02-23 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 2 50 92.3 0.073 16.65 5.3 17719 -3 18.285
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 2.05 93.4 0.192 6.4 3.5
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 3PYG 2 35.562 17719 905 92.2 0.196 0.193 0.1957 0.253 0.254 RANDOM 12.101
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] -0.23 0.73 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.996 r_dihedral_angle_4_deg 17.848 r_dihedral_angle_3_deg 12.81 r_dihedral_angle_1_deg 6.932 r_angle_refined_deg 1.567 r_angle_other_deg 0.923 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.996 r_dihedral_angle_4_deg 17.848 r_dihedral_angle_3_deg 12.81 r_dihedral_angle_1_deg 6.932 r_angle_refined_deg 1.567 r_angle_other_deg 0.923 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2180 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 53
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing