☰ Navigation Tabs
Structure of a Probable 6-phosphogluconolactonase from Mycobacterium abscessus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ICO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 1600mM sodium citrate, Protein 51.9 mg/ml, Cryo protectant 25% ethlyene glycol, Target DB: MyabA.01244.a.A1 PS00890, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.35 α = 90 b = 41.18 β = 90 c = 44.97 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 MARMOSAIC 225 mm CCD 2011-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 1.5 68.18 99.6 0.068 17.07 41365 -3 18.916
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 1.5 1.54 100 0.448 4.37
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 3ICO 1.5 68.18 41364 2082 99.6 0.1926 0.1916 0.2 0.2106 0.2198 RANDOM 14.4893
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] -0.71 0.29 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.047 r_dihedral_angle_3_deg 12.022 r_dihedral_angle_4_deg 11.352 r_dihedral_angle_1_deg 5.895 r_angle_refined_deg 1.379 r_angle_other_deg 0.929 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.047 r_dihedral_angle_3_deg 12.022 r_dihedral_angle_4_deg 11.352 r_dihedral_angle_1_deg 5.895 r_angle_refined_deg 1.379 r_angle_other_deg 0.929 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1828 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 17
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction