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Crystal structure of E. coli glyoxylate carboligase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 2-4 microlitre of protein solution (5-15 mg/ml, 100 micromolar ThDP, 10 micromolar FAD, 1mM MgCl2 and 10 mM quinone Q0) were mixed with equal volume of reservoir solution (0.5% PEG6000, 0.5M NaCl, 40 mM DTT), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 294.K
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.18 α = 90 b = 188.18 β = 90 c = 249.4 γ = 90
Symmetry Space Group P 41 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 4 BENT CRYSTAL 2004-12-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97897, 0.97946, 0.93929 ESRF ID14-4
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 2.7 50 99.2 0.101 0.089 9.43 4.4 122672 -3 37.8
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 2.7 2.8 93.1 0.347 0.28 2.76 2.21
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 MAD THROUGHOUT 2.7 20 122207 2453 99.9 0.22 0.219 0.2231 0.253 0.2553 RANDOM 27.79
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] -0.09 -0.09 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.25 r_dihedral_angle_4_deg 17.681 r_dihedral_angle_3_deg 14.993 r_dihedral_angle_1_deg 5.916 r_scangle_it 1.463 r_angle_refined_deg 1.229 r_scbond_it 1.024 r_angle_other_deg 0.79 r_mcbond_it 0.524 r_mcangle_it 0.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.25 r_dihedral_angle_4_deg 17.681 r_dihedral_angle_3_deg 14.993 r_dihedral_angle_1_deg 5.916 r_scangle_it 1.463 r_angle_refined_deg 1.229 r_scbond_it 1.024 r_angle_other_deg 0.79 r_mcbond_it 0.524 r_mcangle_it 0.504 r_symmetry_vdw_other 0.198 r_symmetry_vdw_refined 0.19 r_nbd_refined 0.184 r_nbtor_refined 0.17 r_nbd_other 0.169 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.127 r_nbtor_other 0.081 r_mcbond_other 0.065 r_chiral_restr 0.064 r_xyhbond_nbd_other 0.02 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other 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 27180 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 548
Software Software Software Name Purpose XSCALE data scaling SHARP phasing SOLOMON phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction