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Crystal structure of putative L-alanine-DL-glutamate epimerase from Burkholderia xenovorans strain LB400
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 294 100mM Tris-HCl pH 8.5, 12% Glycerol, 1.5M Ammonium sulfate, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.18 43.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.906 α = 90 b = 104.906 β = 90 c = 145.658 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 2007-01-20 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 1.8 85.13 93.2 0.109 0.109 16.8 8.8 35232 22.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 56.8 0.825 0.825 0.9 2.3 3054
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.8 20 35192 1755 93.05 0.157 0.156 0.1593 0.192 0.1967 RANDOM 26.362
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 -0.23 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.403 r_dihedral_angle_4_deg 19.024 r_dihedral_angle_3_deg 12.007 r_dihedral_angle_1_deg 5.548 r_scangle_it 3.352 r_scbond_it 2.158 r_angle_refined_deg 1.331 r_mcangle_it 1.231 r_mcbond_it 0.78 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.403 r_dihedral_angle_4_deg 19.024 r_dihedral_angle_3_deg 12.007 r_dihedral_angle_1_deg 5.548 r_scangle_it 3.352 r_scbond_it 2.158 r_angle_refined_deg 1.331 r_mcangle_it 1.231 r_mcbond_it 0.78 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3103 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 10
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing