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Crystal structure of glutamate racemase from Listeria monocytogenes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Jeffamine ED-2001 pH 7.0,
0.1M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.651 α = 90 b = 66.651 β = 90 c = 257.99 γ = 90
Symmetry Space Group P 43 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 ADSC QUANTUM 210r mirrors 2009-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9793 APS 19-BM
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 2.3 50 99.6 0.105 0.105 37.25 17.6 26802 26802 -3
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 2.3 2.34 99.5 0.606 0.606 4.5 15.3 1283
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.3 50 25407 25407 1348 99.66 0.19109 0.19109 0.18844 0.2219 0.24411 0.2752 RANDOM 19.685
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] 0.7 0.7 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.178 r_dihedral_angle_4_deg 17.527 r_dihedral_angle_3_deg 13.818 r_dihedral_angle_1_deg 5.389 r_scangle_it 2.033 r_scbond_it 1.269 r_angle_refined_deg 1.222 r_angle_other_deg 0.863 r_mcangle_it 0.716 r_mcbond_it 0.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.178 r_dihedral_angle_4_deg 17.527 r_dihedral_angle_3_deg 13.818 r_dihedral_angle_1_deg 5.389 r_scangle_it 2.033 r_scbond_it 1.269 r_angle_refined_deg 1.222 r_angle_other_deg 0.863 r_mcangle_it 0.716 r_mcbond_it 0.381 r_mcbond_other 0.101 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4066 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 37
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM model building ARP/wARP model building CCP4 model building O model building Coot model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling DM phasing CCP4 phasing