☰ Navigation Tabs
Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis in complex with ETHYL DIHYDROGEN PHOSPHATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 11EF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 70 mM MES pH 6.5, 70 mM CaCl2, 14% PEG 1500, 8.4% hexanediol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. 20 hour soak in 10 mM glycerol 3-phosphate (D/L mixture), EFS fit best to the electron density, plate Liu-S-202 E9-F10, Puck: PSL-0208, Cryo: 100 mM MES, pH 6.5, 100 mM CaCl2, 20% PEG 1500, 12% hexanediol
Crystal Properties Matthews coefficient Solvent content 2.25 45.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.318 α = 88.44 b = 49.513 β = 83.14 c = 116.429 γ = 86.18
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 9M 2026-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 45.74 95 0.076 0.09 0.048 0.997 10.1 3.6 152470
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 87.9 0.642 0.767 0.414 0.707 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 45.74 1.96 152427 7874 94.93 0.1533 0.1519 0.1614 0.1818 0.1904
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.995 f_angle_d 0.877 f_chiral_restr 0.052 f_plane_restr 0.012 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7549 Nucleic Acid Atoms Solvent Atoms 1014 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction