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Crystal Structure of a Member of the Enolase Superfamily from Salmonella Typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GL5 pdb entry 2GL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 100MM DL-MALEIC ACID, 25% PEG 3350, 50MM MGCL2, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.662 α = 90 b = 140.818 β = 105.94 c = 126.838 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH MIRRORS 2006-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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 50 98.6 0.083 0.072 5.4 3.4 241824 241824 29
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 2.07 96.8 0.46 0.41 1.9 3.1 23617
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 2GL5 2 20 231877 231877 4757 96.84 0.20979 0.20887 0.2093 0.25531 0.2542 RANDOM 33.287
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] 3.01 0.57 -1.24 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.48 r_dihedral_angle_4_deg 20.343 r_dihedral_angle_3_deg 16.284 r_scangle_it 8.978 r_dihedral_angle_1_deg 7.364 r_scbond_it 6.93 r_mcangle_it 5.402 r_mcbond_it 4.476 r_angle_refined_deg 1.249 r_symmetry_hbond_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.48 r_dihedral_angle_4_deg 20.343 r_dihedral_angle_3_deg 16.284 r_scangle_it 8.978 r_dihedral_angle_1_deg 7.364 r_scbond_it 6.93 r_mcangle_it 5.402 r_mcbond_it 4.476 r_angle_refined_deg 1.249 r_symmetry_hbond_refined 0.322 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.235 r_xyhbond_nbd_refined 0.198 r_nbd_refined 0.184 r_chiral_restr 0.108 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24220 Nucleic Acid Atoms Solvent Atoms 1808 Heterogen Atoms 8
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling