☰ Navigation Tabs
Crystal structure of putative L-alanine-DL-glutamate epimerase from Burkholderia xenovorans strain LB400 bound to magnesium and alpha-ketoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GO2 pdb entry 3GO2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.8 294 100mM sodium acetate pH 4.8, 2.4M sodium formate; pH adjusted to 7.0; soaked with 100mM MgCl2 and 100mM alpha-ketoglutarate, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.04 α = 90 b = 105.04 β = 90 c = 144.363 γ = 90
Symmetry Space Group I 4 2 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 ADSC QUANTUM 315 2010-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.97958 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.86 50 99.7 0.084 0.084 29.5 15.2 34329 34226 21.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.89 100 1.4 13.2 1699
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3GO2 1.86 20 34178 27356 868 80.04 0.1619 0.1606 0.17 0.2013 0.2142 RANDOM 29.2587
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] -1.27 -1.27 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.02 r_dihedral_angle_4_deg 16.011 r_dihedral_angle_3_deg 13.472 r_dihedral_angle_1_deg 5.84 r_scangle_it 3.097 r_scbond_it 1.938 r_angle_refined_deg 1.326 r_mcangle_it 1.068 r_angle_other_deg 0.893 r_mcbond_it 0.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.02 r_dihedral_angle_4_deg 16.011 r_dihedral_angle_3_deg 13.472 r_dihedral_angle_1_deg 5.84 r_scangle_it 3.097 r_scbond_it 1.938 r_angle_refined_deg 1.326 r_mcangle_it 1.068 r_angle_other_deg 0.893 r_mcbond_it 0.578 r_mcbond_other 0.153 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3126 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 13
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing